Recent Major Versions:
2024.0
2023.2
2023.1
2023.0
2022.2
2022.1
2022.0
2021.2
2021.1
2021.0
2020.2
2020.1
2020.0
2019.2
2019.1
2019.0
Version 2024.0 (05 December 2023)
Patch Versions:
2024.0.1
2024.0.2
2024.0.3
Features:
- Cloning Validation: Visual and semi-automated validation tool to add, export and record validation metadata
- Map to Reference(s): Interactive quiz to provide guidance and assist in deciding which algorithm to try
Minor Features and Usability Improvements:
- Cloud Database: Now correctly uses custom SSL certificates when set by SSL.CustomTrustedCertificates in advanced preferences
- De Novo Assembly: Added suggestions for alternative assemblers in interactive quiz
Fixes and Minor Changes:
- Back Translate: Fixed bug where it produces no results on some large sequence lists
- Batch Rename: Fixed rare hang when creating advanced batch renames
- CRISPR: Fixed the process to install and invoke Doench 2016
- Change Propagation: Fixed bug where manual edits might cause the change to propagate wrongly
- Cloud Database:
- Fixed a rare crash when creating many folders
- Fixed an occasional hang when displaying the batch rename options
- Improved time taken to login after logging out
- Fixed login error messages sometimes not being fully displayed
- Fixed a crash when closing the login dialog early
- Custom BLAST: Fixed a bug where sometimes users cannot install NCBI custom database
- DeSeq2: Fixed rare crash where annotations with multiple intervals were not compared correctly
- General: Fixed rare crash when Geneious Prime is shutting down
- Import: Fixed a rare issue during import of excel files
- Map to Reference(s): Fixed rare crash
- Search: Fixed a rare bug where searching the menu could crash when a plugin had been removed
- Shared Database:
- Fixed bug that caused Geneious to freeze up after any network problem
- Fixed a rare bug where Prime would not shutdown when it was connected to a shared database
- Increased efficiency of document indexing
- Trim Ends: Fixed incorrect track annotations on trimmed sequences when they are trimmed from within a workflow
Other Notes:
- Java: Updated bundled JRE version to 11.0.20.1+1
Patch 2024.0.1 (30 January 2024)
Fixes and Minor Changes:
- Anneal Oligos: Updated Workflow to correctly display overhangs if they're on the same strand
- Annotation Generators: Fixed an issue where changing settings during annotation prediction produced incorrect results
- BLAST:
- Fixed an issue where a local blast database could be corrupted when its containing folder was moved
- Group hits by original query sequence when exporting to BLAST text format
- Cloning Validation: Fixed a bug where the jump to start and end buttons sometimes did not display
- Contig View: Fixed occasional crash when sorting large contigs
- Import: Fixed a bug where certain characters in GFF sequence names were causing crashes on import
- Lineage: Fixed rare bug that introduces wrong data when manually editing sequences in some cases
- Map to Reference: Fixed a bug where references with many ambiguities were not linked from the results of BBMap
- Primers:
- Fixed a bug where alias documents were not being detected properly when running Test with Saved Primers
- Fixed a bug where copying translated primers could fail
- SAM/BAM Importer: Fixed bug where Hard-trimmed reads would be imported to a wrong location
- Sequence View: Fixed selected annotation changing sometimes after saving changes
- UniProt: Fixed database search
Patch 2024.0.2 (15 February 2024)
Fixes and Minor Changes:
- Import: Fixed a bug where the excel importer failed to import files with non-latin characters
- Map to reference: Fixed crash or incorrect alignment when there is an insertion relative to a structural variant on the end of the reference sequence
Patch 2024.0.3 (06 March 2024)
Fixes and Minor Changes:
- Cloning: Prevent using truncated 'Gibson Primer Extension' during Homology Cloning
- Cloud: Fixed a bug when importing metadata from a CSV into a cloud workspace
- Sequence View: Fixed crash when extracting sequences or consensus from some alignments
Other Notes:
- GSDB: Added support for RedHat 8
Version 2023.2 (13 June 2023)
Patch Versions:
2023.2.1
Features:
- De Novo Assembly: Interactive quiz to provide guidance and assist in deciding which algorithm to try
Minor Features and Usability Improvements:
- Lengths Graph: Added ability to export a csv file with sequence length data
- STAR: Enabled use of sequence lists as references
Fixes and Minor Changes:
- Find CRISPR Sites: Fixed rare crash which occurred with some sequence lists with the "pair-sites" option selected
- Geneious Cloud Database (beta): Fix cases where folder contents were not correctly being downloaded
- Metadata: Fixed a rare crash when modifying document metadata types
Patch 2023.2.1 (25 July 2023)
Minor Features and Usability Improvements:
- De Novo Assembly: Enabled interactive quiz to automatically download an install plugins
Fixes and Minor Changes:
- Cloning Validation: Fixed a rare bug causing crashes and UI issues
- Cloning from Workflows: Fixed a bug where it would set the longest sequence as the first insert despite any prior sorting steps
- Cloud Database: Fix failure to import BLAST result folders
- Import: Fixed a bug where the progress is not shown when importing large zip files
Version 2023.1 (21 February 2023)
Patch Versions:
2023.1.1
2023.1.2
Features:
- Geneious Cloud Database (beta): Added a new cloud database, which provides access to 10GB of free, secure personal data storage
- Import: Added ability to import DNAStar Lasergene SeqBuilder(Pro) .sbd file format
- Dotmatics Platform Integration Plugin: Added a plugin that adds ability to register sequences in Bioregister
Fixes and Minor Changes:
- Annotations: Fixed a bug where some annotations had properties incorrectly reverse complemented
- BLAST: Percentage will no longer display rounded values when they are close but not exactly 100% or 0%
- Cloning Validation: Fixed a rare drag and drop bug
- Document Info: Improved save performance when documents have many metadata sections
- General:
- Increased the Log4j version used by geneious from 2.17.1 to 2.19.0
- Fixed an issue where opening sequence view in a pop-out window does not work sometimes
- PDB Importer: Better handling of PDB files created by RoseTTAFold
- Plugins: Fixed rare crash in Microsatellite plugin
- Primer Design: Fixed included region option not being selected on fresh installs when a region was selected
- Protein Structure Alignment: Fixed overzealous check for multiple models when aligning PDB documents
- Workflows: Fixed a bug where documents exported as TSV contained unselected fields
Patch 2023.1.1 (04 April 2023)
Fixes and Minor Changes:
- BLAST: Fixed a crash when using a sequence that has gaps and qualities as input
- Cloning Validation: Fixed a rare bug where using the filter could cause a crash
- Cloud: Fixed some crashes when logging out of the Cloud Workspace
- Contig View: Fixed occasional crash when sorting large contigs
- DESeq2: Newer versions of Bioconductor are now recognised and supported on Linux
- Import: Primers in DNAStar Lasergene SeqBuilder(Pro) .sbd format are now recognized
- Java: Updated bundled JRE version to 11.0.18+10
- NCBI Structural Database & PDB Import: Fixed a bug where loading PDB documents crashed if Beta Sheets were at positions with index >= 1000
Patch 2023.1.2 (27 April 2023)
Fixes and Minor Changes:
- Geneious Cloud Database (beta): Fix cases where folder contents were not correctly being downloaded
- General: Fixed occasional crash on MacOS after updating Geneious
- SSL: Fixed a bug where Geneious Prime cannot access trusted certificates on Windows
Version 2023.0 (02 November 2022)
Patch Versions:
2023.0.1
2023.0.2
2023.0.3
2023.0.4
Features:
- CRISPR: Added more PAMs to Find CRISPR Sites
- Cloning Validation: Added a new tool for automating sequence alignment during batch plasmid validation
- Primer Design: Added a new tool for primer specificity testing
- STAR: Added STAR, a RNA-seq mapper that performs highly accurate spliced sequence alignment
- Workflows: Added new workflow for batch exporting multiple sequences as individual images
Minor Features and Usability Improvements:
- CRISPR: Enabled selection of individual off-target sequences
- Command Line Interface: Now supports using database folders as inputs
- Geneious Academy: Added a shortcut to the new Geneious Academy in the Help menu
- General: Progress reporting for loading selected documents on network databases no longer blocks user activity
- Preprocessing: BBDuk no longer requires a separate plugin to use
- User Interface: Dropdowns now support filtering and more clearly show when it is possible to enter custom value
Fixes and Minor Changes:
- Annotations:
- Fixed a crash when exporting an annotation table with the "Paired Primer" column
- Fixed pressing delete in the Annotations Table sometimes not deleting the selected annotation(s)
- Bowtie2: Updated to Bowtie2 2.4.5
- CRISPR: Added a maximum gap size option to Analyzing CRISPR Editing Results
- Command Line Interface: Fixed bug where documents in the local database could not be found
- Dark Mode: Brightened the Sequence Viewer selected number color
- De Novo Assembly: Fixed it sometimes producing results containing mismatches when the maximum mismatches settings was set to 0
- De Novo Assembly and Map to Reference(s): Now fails promptly instead of sometimes continuing after running out of memory
- General:
- Reformatted concatenated file names when spacers used
- Creating or renaming a folder will ask for another name in the event the provided name was invalid
- Added a Save as PDF... option to the File menu
- Fixed crash when batch renaming very large sequence lists
- Improved document save performance, especially on network databases
- Fixed a rare crash when gathering system information during start-up
- Group Sequences: Fixed crash when grouping protein sequences together with paired nucleotide sequences
- MAFFT: Updated MAFFT to version 7.490
- MUSCLE: Updated MUSCLE algorithm to version 5.1
- Memory: Reduced memory usage when dealing with some large data sets
- SPAdes: Updated SPAdes to version 3.15.5
- Sample Documents: Added the SARS-CoV-2 genome
- Sequence View: Added option to turn off three letter amino acids when zoomed in on protein sequence views
- Shared Database: Updated default mysql-connector to 8.0.28
- Shared database: Fixed a bug where indexing of documents in shared databases would not proceed due to a corrupt document
- Startup: Added a progress bar to show progress starting Geneious
Other Notes:
- 16S Biodiversity: Removed the 16S Biodiversity tool
- Plugin Development Kit: Fixed return behaviour for DocumentUtilities.getDocumentsByURN() not matching its javadoc
- Public API: Added an API to add stamps to items in dropdowns
- TopHat: Removed TopHat RNAseq mapper
Patch 2023.0.1 (30 November 2022)
Fixes and Minor Changes:
- CRISPR: Fixed a bug where the Doench2016 algorithm would not work for users who had recently installed it
- Cloning Validation: Now supports selection of non-adjacent name parts for automatic grouping and mapping
- Document Table: Fixed name column sometimes not scrolling vertically to match other columns
- NCBI: Fixed Structural Database search failure
- STAR:
- Added support for multiple references
- Improved track names for junctions
Patch 2023.0.2 (10 January 2023)
Fixes and Minor Changes:
- BLAST: Fixed incorrect annotation placement with a translation BLAST when gaps are present
- Map to Reference: Fixed a bug which would cause Map to Reference to sometimes freeze when loading the options
- Shared database: Fixed issue where some users were not able to save files
Patch 2023.0.3 (18 January 2023)
Fixes and Minor Changes:
- BLAST: Fixed crash introduced in 2023.0.2 when a graph query needs to have a gap inserted
- Primer Design:
- Fix crash when checking offsites with too many similar regions
- Prevents options from having negative values to avoid a crash
Patch 2023.0.4 (26 January 2023)
Fixes and Minor Changes:
- Fixed a bug where new metadata types are not saved properly when documents are moved to a new database.
Version 2022.2 (14 June 2022)
Patch Versions:
2022.2.1
2022.2.2
Features:
- CLI: Added support to import and export files from local databases
- CLI: Added support to import and export files from shared databases
- Cloning: Added In-Fusion cloning
- Parts Cloning: Added support for protein documents
- Primer Import: Added the ability to automatically annotate primer extensions on import if provided appropriately formatted sequences
Minor Features and Usability Improvements:
- 3D Protein viewer: Updated Jmol to version 6
- Cloning:
- Improved input validation for batch operations
- Improved the cloning options dialog
- Improved the naming scheme for sequence list results of cloning operations
- Other various UI/UX improvements
- User Interface:
- Added filter functionality to combo box components with 10 or more values
- Added floating name column to document and annotation tables
Fixes and Minor Changes:
- Advanced Preferences: Fixed advanced preference table values not being reloaded after changes
- Apply Variants to Reference Sequence: Added option to mask low coverage regions with N
- BLAST:
- Fixed bug where changing options in BLAST workflows for one blast type affected other blast type options
- Chromatogram Viewer: Fixed a bug where some Color Schemes were showing incorrect line and text colors
- Cloning:
- Fixed a bug where cloning results had the wrong insert order in their names
- Fixed canceling operations
- Fixed rare crash where rearranging cloning inserts in restriction cloning
- Operations should now perform significantly faster on large datasets
- Sequence Lists are now reversed correctly in Golden Gate cloning
- Sequence Lists produce correct lineage interval in Golden Gate cloning
- Command Line Interface:
- Added parameter --installationId to display installation id in command line
- CRISPR:
- Better detection of pre-installed python3
- Fixed annotation colors not showing up sometimes when Find CRISPR Sites is run on sequence lists
- Prevented attempts to install an incompatible version of python
- Databases
- Improve performance when copying multiple documents and folders in the local database
- Geneious Server: Now ensures python3 is available for SPAdes
- General:
- Added a button to hide/show text on all password fields
- Added ability for admins to disable arbitrary plugins
- Fixed a bug where ctrl+drag (or alt+drag) documents into the same folder and choosing 'Replace' deletes these documents
- Fixed occasionally being unable to uninstall Geneious
- Fixed a rare crash when gathering crash information
- High/Low Coverage Finder: Changed annotation type to be always "Coverage - Low" instead of sometimes "Coverage - Low" and sometimes "Low" and likewise for high coverage annotations
- Import/Export:
- Fixed a bug where document and folder chooser dialogs do not appear when Grammarly Desktop is installed or system screen zoom settings are enabled
- Fixed rare crash when importing vcf files with malformed meta-info data
- Geneious now sorts sequence annotations by sequence start index when exporting in GFF and BED file formats
- Sequences that have metadata in comments can now be grouped during import
- Licensing: Fixed rare error whilst checking Sassafras license
- Map to Reference:
- Fixed a rare case where Map to Reference introduces a gap 1 bp from the end of the sequence
- Fixed references to input reads being discarded sometimes when mapping to a circular reference sequence
- Optimize Codons: Fixed a rare crash when running optimize codons on a sequence list
- Plugins: Fixed issue where disabling a plugin that another plugin was dependent on caused a failure to start
- Plugin Developer Kit:
- Added Logs class to allow developers easy access to standard Geneious logs
- Fixed a crash when importing multiple files from the wrapper plugin
- Public API: Marked deprecated methods
- Sequence View:
- Fixed a rare case where all annotations may disappear from the sequence view
- Save as PDF: Fixed bug on macOS where saving as PDF would send to the local printer
- SPAdes: Use python3 by default on MacOS
- User Interface:
- Cloning reports are no longer light themed when viewing in dark mode
- Fixed bug where drag and drop was not showing the correct colors in light mode
- Fixed bug where text in the document table could show as multi-line text when the table was resized
- Fixed UI error where some annotations were not visible in Text View
Patch 2022.2.1 (12 July 2022)
Minor Features and Usability Improvements:
- Annotation Table: Added columns for paired primers and associated probes
Fixes and Minor Changes:
- Cloning: Reduced the number of dialogs associated with poor quality primer generation warnings when batch cloning
- Command Line Interface: Fixed bug where documents in the local database could not be found
- Import:
- Fixed error where tutorials with subfolders could not be imported
- Folder indexing now needs to be complete before allowing metadata import
- Primers: Fixed bug where a Probe or Primer was not paired with Primers that have an extension added
- Search: Fixed vertical scrollbar visibility
- User Interface: Fixed right click menu on Mac showing too far on the right
Patch 2022.2.2 (23 August 2022)
Fixes and Minor Changes:
- Annotations: Fixed a bug where running a cloning operation would reset custom annotation colors
- CRISPR: Fixed failure to install Doench 2016 algorithm
- General: Fixed a bug preventing fastq files from being imported into Shared Database and Geneious Server Database
- Shared Database: Fixed a bug preventing copying folders under some circumstances
Version 2022.1 (15 February 2022)
Patch Versions:
2022.1.1
Features:
- Batch Golden Gate: Golden Gate cloning now understands List documents if they contain sequences that are in the same direction
- Parts Cloning: Added functionality to support parts cloning, for generating combinations of sequences from existing parts
- Primer Import: Updated to import sequences from excel files
Minor Features and Usability Improvements:
- Dark Mode: Many small adjustments have been made to improve the user experience
- De novo assembly: Improved performance on Geneious de novo assembly, especially on high coverage data sets
Fixes and Minor Changes:
- Annotate by Blast: Fixed an occasional crash when running operation on multiple sequences at once
- Automatic Update: Fixed a bug where automatic update dialogs were incorrectly presented to the user
- BLAST:
- Fixed a bug in Custom BLAST where databases with spaces in the name could not get the full sequence
- Updated to BLAST+ 2.12.0
- Command Line Interface:
- Added --multi-file/-m advanced flag to export multiple result documents as individual files
- Fixed a bug where CLI was crashing on some headless Linux environments
- Fixed irrelevant error messages being occasionally printed
- Moved "--include-id" command into advanced help instead of basic help
- Back Translate: Fixed a crash when performing this operation on protein lists using "Selected Region"
- Dark Mode: Fixed a rare bug on macOS which caused a hang when restarting after switching between themes
- Digest into Fragments: Digested annotations are now properly truncated to fragment length with correct intervals
- Gateway Cloning: Improved the accuracy of our Att Site Finder and added support for different site variants
- Geneious Server: Fixed a rare bug where the progress is not set as complete for finished remote jobs
- Import:
- Files exported from SnapGene should now have their name imported also, instead of 'Exported'
- Fixed a bug importing Newick files containing very deep trees
- Merged Paired Reads: Merged output document description mentions how many pairs were merged
- Optimize Codons: Fixed bug where some read-only annotations were transferred to the optimized document
- Options profiles: Now shows an error message instead of silently failing when an options profile can't be restored
- Primers:
- Fixed a bug where DNA probe annotations had missing fields
- Fixed a bug where edited sequences converted to oligo sequences would not update their melting temperature in the document panel
- Fixed a bug where mismatched primers could be merged together in the "Test with Saved Primers" operation
- Sequence View:
- Fixed a bug where selections were not saved on the source sequence after extracting or translating
- Fixed a rare crash when undoing changes to read only annotations
- Set Paired Reads: Fixed misleading error message when using this from Workflows on data which can't be paired
- Statistics: The length statistic no longer counts gaps and stop codons on protein sequences
Other Notes:
- Java: Updated bundled JRE version to 11.0.14+9
Patch 2022.1.1 (15 March 2022)
- Java: Updated bundled JRE version to 11.0.14.1+1
- Licensing: Licenses should now behave correctly once entered into Geneious. Please contact our support team if you are still encountering any licensing issues
- Parts Cloning: Fixed a bug with propagating changes to parent documents
- Shared Database: Fixed bug where folders in the root directory could not be renamed
- Usage Logging: Fixed a rare bug that caused Geneious Prime to hang when the user interacted with the UI if anonymous usage tracking was enabled
Version 2022.0 (12 October 2021)
Patch Versions:
2022.0.1
2022.0.2
Features:
- Annotate by BLAST: Added the option to annotate regions of your sequence using BLAST (option can be found in the Annotate & Predict menu)
- Command Line Interface: Released version 2022.0
- Dark Mode: Added Dark Mode Beta theme which can be turned on in Preferences
Minor Features and Usability Improvements:
- Advanced Preferences: Added filter
- Chromatogram Traces: Added option for highlighting regions of traces which do not match base calls
- Experimental Features:
- Added 'Experimental Features' section to preferences with new functionality for Search Everywhere and filtering while editing annotations
- Optimize Codons: Added the option to apply/revert an optimized codon to the annotations context menu
Fixes and Minor Changes:
- Alignment View:
- Fixed occasional crash when extracting a sequence from an alignment
- Characteristics for selection:
- Fixed crash when selected primer pairs are facing the same direction
- Removed option to test as pair if selected primers face the same direction
- Contig View:
- Fixed hang selecting a region in the consensus sequence before it has finished calculating
- Fixed poor performance on very high coverage contigs
- De novo assembly: Fixed rare crash after pressing the 'Stop' button
- Document View:
- Fixed a rare crash and increased the reliability of selections when switching between different document views
- Moved column preferences button to the status bar and redesigned menu layout
- Export:
- Fixed an occasional crash while exporting csv documents
- Fixed a rare issue on Windows where export dialog may hang indefinitely
- General:
- Fixed bug where documents are sometimes not selected when they should be
- Improved detection of faulty hardware and showing a message explaining the problem instead of crashing
- Improved detection of local database folder stored within file sync folders
- Import:
- Fixed a bug when importing tree files with newick format attributes
- ZIP file import (containing files of any format supported by Geneious) now also works on files which have had their extension changed from
'.zip' to '.geneious' (useful for external software to create files which will be opened in Geneious)
- Licensing: Fixed bug where users cannot configure Floating License Manager details in admin properties
- Map to reference: Fixed crash in rare cases when a large gap spans the origin of a circular reference sequence
- Metadata Importer: Fixed column match not working on alias documents on shared databases
- Operating System:
- macOS: Fixed a FlexNet group license activation issue if a switched-out-user on the machine has Geneious Prime open in the background
- macOS: default_user_preferences.xml can now be loaded from ~/Library/Application Support/Geneious/ directory
- macOS: geneious.properties can now be loaded from ~/Library/Application Support/Geneious/ directory
- Optimize Codons: Fixed crash when using a space at the end of the forbidden custom motif option
- Primer Design: Users are now warned if the primer Dimer Tm is above the Max Dimer Tm limit set in options (caused by an extension)
- Search: ‘Include Subfolders’ selection state is now shared between basic and advanced search
- Sequence View:
- Fixed crash with copying annotation names when duplicate meta data fields are present
- Fixed incorrect primer Tm shown in preview box in some cases
- Fixed rare crash when using 'Pair Selected Primers'
- The ‘add primer annotation’ button will now correctly show up after selection ends are adjusted with the mouse
- User Interface: Dropdown arrow added to buttons
- Virtual Gel:
- Added indication for supercoiled DNA displayed as linear
- Fixed crash in print preview dialog and ‘Save to Image’ with a lot of lanes
Other Notes:
- Java: Updated bundled JRE version to 11.0.12+7
- Java: Geneious and the Plugin Development Kit now use JDK 11
Patch 2022.0.1 (16 November 2021)
- Chromatogram Traces: Improved accuracy and visibility of chromatogram regions which do not match their nucleotide calls
- Import:
- Fixed a crash when importing SnapGene files with 'het' features
- Better handling of Helix, Sheet & Turn types when importing SnapGene protein files
- Tree Viewer: Fixed a bug preventing users from changing the line weight
- User Interface: Upgraded to FlatLaf 1.6
- Workflows: Fixed a crash when dragging and dropping workflow steps in the editor
Geneious Server and Geneious Server Database:
- Updated installation scripts and manual
- Updated to JRE 11
- Updated to Tomcat 9
- Support for CentOS 6 and RHEL 6 has been discontinued
Patch 2022.0.2 (27 January 2022)
- Annotate by Blast: Fixed an occasional crash when running operation on multiple sequences at once
- Command Line Interface:
- Fixed a bug where CLI was crashing on some headless Linux environments
- Fixed irrelevant error messages being occasionally printed
- Dark Mode: Fixed a rare bug on macOS which caused a hang when restarting after switching between themes
- De novo assembly: Fixed sequences not assembling together sometimes when duplicate sequences with duplicate trimmed regions were present
- log4j: Migrated codebase from log4j version 1.2 to the secure log4j 2.17 (there is no risk of data breach and Geneious Users have not been affected by the recent log4j vulnerabilities)
- Plugin Development:
- Added API documentation
- Fixed a bug where plugins were not checked for updates
- SPAdes Assembler: Fixed bug affecting assembler on macOS Monterey
- User Interface: Fixed bug where filter panels were occasionally minimized
Version 2021.2 (15 June 2021)
Patch Versions:
2021.2.1
2021.2.2
Features:
- Gel:
- Improved lane heading usability and displayed enzymes
- Allowed fragment view on multiple sequences
- Added support for multiple sequences
- CRISPR: Displayed CRISPR cut sites for SpCas9 and LbCpf1/AsCpf1 with default PAM sites
- Sequence View: Geneious now indicates a premature stop codon on CDS annotations
- Annotations: Annotation names and properties can now be batch copied from other annotation,
sequence, or document properties
Minor Features and Usability Improvements:
- CRISPR: Added support for macOS Big Sur machines by using the latest Python 3.9
- De Novo Assembly:
- Improved performance and accuracy of Geneious de novo assembler when duplicate reads are present
- Upgraded bundled SPAdes version to 3.15.2
Fixes and Minor Changes:
- Alignment View:
- Fixed out of frame translation in annotation tooltips when annotation starts on a gap
- Fixed crash after editing the consensus sequence, then turning off the consensus sequence, then using
undo
- Fixed crash trying to drag nucleotides around while an operation is running on the alignment
- Annotations:
- Each row in the annotations table now has a checkbox to make selecting multiple annotations easier
- Fixed crash in some situations when selecting many annotations in a long sequence (1 billion bp)
- BLAST:
- Fixed a rare crash when downloading blast hit results from NCBI
- Fixed bug where multi-part databases might be loaded as separate databases into Geneious
- Contig View: Fixed crash sometimes when printing or saving an image when the color scheme is "Mapping Quality"
or "# of mapped reads"
- CRISPR:
- Displayed enzyme name on track and tooltip
- Fixed Find CRISPR Sites occasionally crashing on sequences with ambiguities
- De novo assembly: Fixed crash in rare situations when re-assembling an existing contig
- Export:
- Added support for exporting sequences within alignments in csv/tsv format
- Fixed crash if a document is deleted while exporting or copying the folder which contains the document
- Fixed crash when saving some document view's to PDF
- File Associations: Associated GenBank .gb, .gbk files with Geneious Prime (for non-MSI installers)
- Find Repeats: Fixed occasional crash or incorrect results around the origin of circular sequences
- Geneious Server: Fixed bug where Geneious would sometimes incorrectly state "The selected algorithm is not
supported in the selected location"
- General:
- Fixed crash sometimes due to file synchronization software creating conflict files inside a Geneious
database
- Fixed crash when saving in some situations after copying and pasting sequence fragments within a
sequence which is actively linked to other sequences
- Fixed rare crash on startup or when creating a new folder on computers with unreliable file systems
- Fixed rare crash on startup when a proxy network is configured
- Fixed rare hang on startup on some computers
- Improved performance of drop down options with lots of values
- Prevented crash when data corruption is detected due to a hardware fault and recommend running system
hardware tests
- Import:
- Fixed a crash when importing multiple SAM/BAM/FASTA files together
- Fixed crash in some situations when importing a fastq file containing a sequence over 100 Mbp
- Fixed crash when importing paired read fastq files when at least one of the files contains no sequence
data
- Licensing: Fixed bug where sometimes users cannot share group license in the same machine
- Map to reference: Fixed crash in rare situations
- Mauve Alignment: Fixed crash when Mauve generates an alignment containing invalid nucleotides
- Minimap2: Fixed incorrect unused read count in assembly report when not saving the list of unused reads
- Operating System:
- Fixed crash when macOS Big Sur goes into sleep mode while Geneious Prime is running
- Fixed occasional crash when Geneious hangs on macOS Big Sur
- Plugins: Improved detection of when problems are due to external plugins and crashes now suggest uninstalling
the problematic plugin
- Primer Design: Fixed undo/redo shortcut keys crashing "Primer Sequence" field when editing primer annotations
- Search:
- Fixed rare crash when searching and shutting down Geneious with a shared database connection
- Fixed rare crash when searching when the document table is not showing
- Sequence View:
- Fixed annotation tooltip sometimes disappearing when you try to select text within it
- Fixed hang on zero length circular sequences
- Fixed crash and/or excessive numbers of dialogs showing when annotating hundreds of sequences with
different track names
- Fixed crash in rare situation when reverse complementing a sequence
- Fixed incorrect translation to Methionine of first codon in annotation tooltips and codon usage
statistics when annotation is truncated
- Fixed rare crash pairing or unpairing primers on a read-only document
- Fixed rare crash when attempting to view some sequences which contain many tracks
- Fixed rare crash when filtering annotations
- Fixed rare crash when viewing primers with extensions
- Fixed translate button crashing or generating a nucleotide sequence when primer pairs are selected
- Fixed various rendering bugs when wrapping is on when there are primers with an overhang before the
beginning of the sequence
- Restriction sites cut position indicators are now larger
- Test with Saved Primers: Fixed counter for number of primer results generated
- User Interface:
- Fixed rare crash when selecting multiple items in the service tree
- Fixed miscellaneous bugs
- Upgraded to FlatLaf 1.2
- Volcano Plot: Fixed a crash when generating a volcano plot with only invalid annotation qualifiers
- Workflows: Fixed crash pressing enter in add operation filter when there are no operations matching the filter
Other Notes:
- Java: Updated bundled JRE version to 11.0.11+9
- Plugin Development:
- Added documentation to all database API methods for whether or not they may be called from the Swing
thread
- Fixed crash in ExampleDocumentViewer when looking at RNA and Protein documents
Patch 2021.2.1 (13 July 2021)
- Analyze CRISPR Editing Results: Fixed incorrect summary statistics for
reads which are truncated 1 or 2 bp before the end of the variant region
- Contig View: Fixed poor performance viewing large contigs when amino
acid numbering is turned on
- Export: Added support for exporting sequences within alignments in
csv/tsv format
- MSI Installer: Fixed a bug where file associations where not set during
install process
- Plugin Development: Fixed bug preventing use of all supported file
formats (e.g. csv) as input to wrapper plugins
- Premature Stop Codons: Fixed display on protein sequences
- Shared Database: Improved speed when using databases with a large number
of documents
- Text View: Changing options no longer causes a crash on empty sequences
Patch 2021.2.2 (20 July 2021)
- Alignment View: Fixed incorrect primer Tm preview when selecting a region containing gaps
- Fragment View: Fixed application hang when selecting large NGS datasets
- Sequence View: Fixed copy-pasting multiple circular sequences of varying length where they weren't being copied correctly
- Sequence View: Fixed rare crash when editing sequences with CDS annotations
Version 2021.1 (16 February 2021)
Patch Versions:
2021.1.1
Features:
- Filter: Re-introduced filter functionality to the document table
- Sequence View:
- Added option to show amino acid numbering to the translation options
- Can adjust the bounds of a selected region within a single sequence by dragging the ends of a selection
- Statistics: Added A[280] of 1mg/ml correction factor to protein and nucleotide translation statistics
Minor Features and Usability Improvements:
- Geneious Server Database: requireUnixAccounts property added to allow users to log in without Unix account on server
- Shared Database: Added 'database-port' property to geneious.properties to configure port, when database uses a port other than the default one
- Search: Re-designed basic search
- Update Process: Improved update speed on Windows and Linux
- Workflows:
- Editing is now non-modal so it is easier to test workflows without closing and reopening them
- Automatic export now includes dependent workflows
- Added new menu item for running custom Java code
- Custom Java code has new simpler entry points for common sequence editing tasks and shows line numbers
Fixes and Minor Changes
- Augustus Plugin: Fixed problem preventing it from working in Geneious Prime 2021
- Export and folder copy: When some documents can't be accessed, can now optionally continue exporting the accessible documents
- File Import: Files imported from a zip archive now have the original zip file as their "imported from" source
- GenBank Import/Export: Fix to ignore importing/exporting the direction of single point annotations
- Geneious Cloud Plugin: No longer bundled with Geneious
- General: Fixed bug on systems with multiple screens on Windows where sometimes the main Geneious window would not appear when starting Geneious
- Import: Fixed dragging and dropping files into folders not working without first clicking on the folder tree
- Local BLAST: Default blast updated to the latest version
- Mauve Alignment: Prevented creating or viewing of invalid alignments
- Operating System:
- macOS: Fixed GateKeeper warning "Geneious Prime.app can't be opened because Apple cannot check it for malicious software" on M1 devices
- macOS: Fixed Geneious Prime constantly crashing after system restart on Big Sur due to max memory changes in Info.plist
- macOS: Max memory settings is now set in '~/Library/Preferences/Geneious.in.use.vmoptions' rather than editing Application 'Info.plist'
- ORF Finder: Fix double annotations generated over the same interval on different reading frames
- Primer Design: Fixed crash in "Primer Sequence" field when editing bases
- SAM/BAM Import: Fixed crash when importing when out of disk space
- Search: Fixed poor performance when selecting which field to search for from the drop down list
- Sequences: Fixed some cases where copy pasting a sequence selection into a text editor would copy paste an entire document
- Sequence View: Fixed annotation popup dismissing occasionally as you move the mouse towards it to select and copy the contents
- Sequence View: Fixed crash when protein sequences contain restriction site annotations
- Sequence View: Fixed incorrect ORF finder results after changing whether a sequence is circular
- Sequence View: Fixed rare crash when editing annotations
- Sequence View: Fixed sequence names being drawn unnecessarily truncated sometimes
- Sequence View: Improved performance adding primer extension restriction sites and when working with large lists of genomic sized sequence
- Spreadsheet Import: Fixed a bug when importing documents with a topology field
- Text View: Clicking "Copy Full Sequence" button should no longer occasionally cause crashes
- Text Viewer: Fixed rare crash when using text viewer on large PDB data
- VNTI/Rebase Importer: Fix occasional crash when importing VNTI database or enzyme documents before Geneious' internal enzyme list is initialised
Other Notes
- Plugin Development: Fixed wrapper plugin crash when using the 'write each input sequence to a separate file' setting on alignments
Patch 2021.1.1 (16 March 2021)
- Analyze CRISPR Results: Fixed crash when run on chromatograms without quality scores
- Annotation Export: Fixed a bug when exporting annotation property values to CSV when the property contained a comma
- Dotplot: Fixed viewer initialisation on macOS
- General: Fixed main window not staying in its maximized state after restarting Geneious
- Primer Design: Fixed bug that prevented continuing in some circumstances on circular sequences
- Sequence View: Fixed crash when editing annotations in tracks in BLAST results
- Text Viewer: Fixed the Text Viewer crashing when the NCBI plugin wasn't available
- Workflows: Fixed new custom Java code methods introduced in 2021.1.0 not compiling
Version 2021.0 (29 October 2020)
Patch Versions:
2021.0.1
2021.0.2
2021.0.3
Features:
- User Interface:
- Redesigned user interface for Geneious Prime
- Changed Geneious default font to Noto Sans
- Updated icons
- Sequence View: Added options to highlight restriction sites affected by Dam, Dcm, or EcoKI methylation
- Statistics: Most Sequence View statistics are now available as fields in the document table
- CRISPR: New scoring strategy for on-target activity, proposed by Doench et al 2016
Minor Features and Usability Improvements:
- Geneious Update: Streamlined the updating experience
- Genetic codes: Added new genetic codes available on the NCBI list
- GenBank Import: Added support for importing metadata from comments
- Menus:
- Add and Export menu buttons added to main toolbar
- Contact Us button moved to Help menu button in the toolbar
- Back Up button moved to Export menu button in the main toolbar
- Restriction Cloning: Labels for selected restriction sites made more obvious
- Shared Database Documents: Shareable links enabled on shared document/s by accessing right click menu item “Copy Document Link”
Fixes and Minor Changes:
- Alignment View: Fixed rare crash when extracting an alignment from an alignment
- Apply Variants to Reference Sequence: Fixed crash when reference sequence has an insertion variant on the end of it
- Batch rename: Fixed bug when used from workflows where some fields were not available to use as a source for building the new value of the field to rename
- Cloning: Primer characteristics now include the extension
- Contact Support: Fixed a bug where our feedback server was occasionally unavailable
- General: Fixed memory leak which caused Geneious to use an extra 1 MB of memory for every 100 documents previously viewed until Geneious is restarted
- General: Improved performance when working with thousands of selected documents
- Identify Organism Workflow: Now supports running on protein sequences
- Import/Export: Updated Genbank annotations
- Local Blast: Fixed a bug which was causing tracks to be hidden in local blast results
- Metadata Importer: Fixed crash while preview is being generated
- Metadata Importer: No longer showing "failed to use some potential references" dialog when no documents match
- NCBI BLAST: Updated BLAST to use the latest NCBI limitations
- Operating System: Fixed crash when MacOS11 goes into sleep mode while Geneious Prime is running
- Plugin Installation: Fixed failure to install plugins if # is part of the operating system user name
- Primers: Fixed crash when placing primer pairs at the origin of a circular sequence
- Restriction Enzymes: Improved handling of duplicated enzymes
- Search: Improved performance when searching local documents
- Search: "This Folder" no longer shown as an option in search when the selected service is not a database folder
- Sequence View: Added an 'Edit: ' prefix to the automatically created Insertion, Deletion, and Replacement annotation types
- Sequence View: Fixed crash occasionally when using "Circular Overview"
- Sequence View: Fixed crash when cancelling Annotate & Predict operations on large data sets with unsaved changes
- Sequence View: Fixed crash when foreground and background residue colors are very similar
- Sequence View: Fixed primers overhanging the end of the sequence sometimes causing it to start at 0% zoom and the zoom in button not working
- Sequence View: Fixed rare crash when changing between sequences in the sequence viewer
- Sequence View: Scrolling an entire page at a time now has a very small overlap with the previous page
- Shared Database: Added MS SQL Server support for Named Instances in the host name
- Shared Database: Disconnecting from a shared database no longer leaves hanging connections
- Tree View: Fixed rare crash when displaying large files
- VNTI GenBank Importer: No longer overwrites feature annotations with comment annotations
Other Notes:
- Java Version: Updated bundled JRE to 11.0.9
Patch 2021.0.1 (01 December 2020)
- CRISPR
- Doench 2016 algorithm annotations now show which version of Python was used
- Modified the Doench 2014 on-target scoring algorithm to give an undefined score for CRISPR sites with ambiguities
- The user is now asked to confirm before any Python modules are installed
- Various options and dialog improvements
- GenBank Import:
- Fixed a bug where a circular sequence is imported as linear sequence if the LOCUS line has a wrong date format
- Updated to correctly import GenBank files with date format yyyy-MMM-dd
- General: Improved performance when creating many folders
- Meta-Data: Fixed incorrect display of meta-data values containing _01 to _05
- Sequence View: Fixed crash reverse complementing a zero length GenBank sequence
- Shareable Links: Added support for spaces and other special characters when pasting the shareable link into browsers such as Google Chrome
- User Interface: Miscellaneous refinements
Patch 2021.0.2 (22 December 2020)
- Genbank Import: Fixed bug which prevented grouping sequences (without metadata) into a list on import
- General: Fixed folders sometimes moving to another location when contracting sub-folders
- Linux: Fixed Geneious running as root in some cases
- NCBI Blast: Fixed downloading full hits from the PDB database
- Plugins: Disabled loading of CrossOver plugin (a plugin which contains a bug which prevents Geneious 2021.0
from starting)
- Sequence View: Fixed crash when changing annotation interval direction
- Sequence View: Fixed crash when drag selecting a region in a sequence over 1 billion base pairs
- Sequence View: Fixed inability to select and copy text from annotation tooltip popup
Patch 2021.0.3 (23 December 2020)
- Sequence Viewer: Fixed crash occasionally when showing an annotation tooltip
Version 2020.2 (16 June 2020)
Patch Versions:
2020.2.1
2020.2.2
2020.2.3
2020.2.4
2020.2.5
Features:
- New tool to Analyze CRISPR Editing Results
- Align and cluster NGS sequencing reads from the results of a CRISPR editing experiment
- Supports a variety of applications including HDR, NHEJ and base editors
- Visualize variants compared to the unmutated reference sequence
- Analyze the frequency of variants and their protein effects
- Enhanced Search Interface
- Search folders and documents from a single unified interface using text queries in real time
- New functionality to search for analysis tools (Actions) available within Geneious Prime
- Easily access additional advanced search options
- Quick access to recently viewed folders and documents
- Codon Optimisation Improvements
- Informative tooltips on Optimized Codon annotations give information about synonymous codons and their frequencies in the chosen codon usage table
- Annotation properties including directionality and CDS codon_start information are now taken into account when optimizing regions chosen by selecting annotations
- When optimizing a selected annotation with multiple intervals, the selection is optimized across intervals and codons are allowed to span adjacent intervals
- When optimizing a reverse-directed selected region, the reverse complement sequence is now optimized
Minor Features and Usability Improvements:
- Document Lineage: Maintain active links between documents when adding, editing or deleting annotations on child documents
- Back and Forward Buttons
- History is persistent between Geneious sessions
- Use shift click to go back and forward between folders instead of documents
- Annotation Tracks
- Annotations in tracks now include a link to track properties in the annotation tooltip
- Heatmap color schemes can now be customized
- Set default translation frame settings for all documents in Sequence View
- Virtual Gel: Can now rearrange lane order on the gel by dragging
- Import protein sequences in SnapGene .prot file format
- Restriction Cloning Usability Improvements
- Default fragment selection for backbone sequences improved, including selection of the larger fragment and avoiding internal cut sites
- Enhanced visual indication of the sequence fragment which is selected for cloning in the preview panel
- Automatic selection of compatible enzymes when adding new inserts to reaction improved
- Sequence length for cloning operations now limited to a maximum of 100kb - limit can be adjusted in advanced preferences by changing Cloning.maximumAcceptedSequenceLength
- NCBI database searches for text queries and NCBI BLAST can now be enabled/disabled independently of each other
- Improved accuracy of consensus calling in the presence of Sanger heterozygotes
Fixes and Minor Changes:
- Align/Assemble
- Map to Reference: Unused reads document produced include the 'Sample' field that was previously only present on the contigs produced
- Minimap2: Fixed crash when using assemble by name
- Fixed Assemble by Name to store a link from the contigs produced to the reference sequence source
- Clustal Omega: Fixed crash when using this after manually editing the 'Command Line' meta-data type
- Annotate and Predict Menu: changed the ordering of menu items to be grouped more logically
- Back Translate: Fixed a bug where annotations could appear in the wrong place when back translating a selected region of a protein
- BBTools: Updated to version 38.84
- BLAST and NCBI Search
- Fixed a rare crash which occurred sometimes when BLAST searching on a local database with long file names
- Fixed crash or corrupted query centric alignment when copying BLAST results into folders containing other BLAST results
- Updated to display correct values for hit tables when tblastn(AA query,DNA database) against a database which is results of a blast
- Fixed bug where tblastn results sometimes had the Molecule Type field set to DNA for pairwise amino acid alignment results
- Prevent searching NCBI for empty accession numbers
- Chromatogram Sequences: Fixed incorrect rendering when mapped to long (million bp +) reference sequences
- Command line tools: Fixed reported output from command line tools (e.g. Flye) containing a duplicated section of text occasionally
- Expression Analysis:
- Fixed failure to install DESeq2 on some Windows machines due to interference from virus scanner
- Prevent crash in Volcano Plots when an annotation doesn't have a name
- Import/Export
- Genbank Export: Now exclude restriction sites from the exported list of features
- Genbank Import: Fixed typo in VNTI Genbank format import feature key - feature type 29 will now import as annotations of type ‘promoter eukaryotic’ instead of ‘promoter uukaryotic'
- Genbank Import: Fixed hang when importing Genbank files containing large COMMENT sections
- Genbank Import: Primer extensions and mismatch information are now imported correctly from SnapGene Genbank format files (.gbk)
- SnapGene .dna file import: Invalid nucleotide characters in primer sequences will now cause import to fail gracefully with a useful error message
- Spreadsheet Sequence Import: Now prevents primer import if primer extension data contains invalid residues
- SAM/BAM Import: Sample name is now imported as the 'Sample' field in Geneious so that variant calling and expression analysis work correctly on mappings with multiple reference sequences
- SAM/BAM Import: Fixed crash when importing SAM/BAM files which reference sequences names that don't belong in any sequence lists in the folder imported into
- Multi file Import: Fixed a bug which would cause crashes in some cases when trying to import multiple files of different types in bulk, for example a .caf file with another file
- Genbank Submission: Fixed "citation date is in future" error when submitting to Genbank sufficiently early in the day in time zones ahead of GMT.
- Metadata: Fixed hang or poor performance when selecting a sequence, during shutdown, or during Genbank export when large meta data fields are present on a sequence
- ORF Finder:
- ‘Continue outside sequence’ fixed to begin ORF annotations outside the sequence where appropriate
- Fixed ‘Continue outside sequence’ generating erroneous ORF annotations with internal stop codons
- Primer Design: Fixed occasional crash with long paired primers on circular sequences
- Restriction Enzymes: Prevent crash during Geneious startup when an invalid enzyme file is being loaded
- Search: Updated advance search to allow searching for custom boolean fields
- Sequence View
- Now uses 3D structure annotation images (alpha helix, beta sheet) for Uniprot files like it previously only did for Genbank files
- Fixed sequence viewer switching to low quality rendering after dragging a track
- Fixed extracting a track annotation as an active link causing the annotation to become duplicated
- When showing the translation for overlapping ORF/CDS annotations which have different frames, it now uses the translation frame of the selected annotation.
- Fixed crash sometimes after editing the same sequence prior to saving changes from two different windows.
- Fixed crash if advanced preference SequenceViewer.maximumZoomOrScrollAnimationDuration is set to 0
- Text View
- It is now possible to display metadata fields in Genbank format
- Non-default Genbank display options are now applied properly when copying to the clipboard or saving as play text
- Fixed bug where changes to the display options didn't take effect when ‘OK’ was pressed when displaying Genbank format
- Fixed a bug where sequence documents with HTML tags in the name or description fields weren't displayed completely
- General
- Startup performance when local documents contains thousands of folders improved
- Fixed memory leak which caused Geneious to use an extra 1 MB of memory for every 100 documents previously viewed until Geneious is restarted
- Fixed crash when attempting to rename a folder after deleting it
- Fixed crash which occurred occasionally when shutting down Geneious
- Wrapper Plugins
- Fixed errors attempting to run some wrapper plugins such as Clustal Omega and Flye when Geneious Prime was installed as root on Linux
- Fixed crash if the wrapped program is not bundled with the Geneious plugin
- DevKit: Fix crash in ExampleDocumentViewer when viewing non nucleotide sequence documents
- Public API: Added a new method to get all the divider locations in a main menu
Shared Databases
- Oracle 19c is now supported
- Added compatibility with MySQL 8 using the included MySQL Java Connector/8.0 which is compatible with MySQL 5.6 and higher. Current users of MySQL Java Connector/5.1 will need to set the Driver Class name in their connection settings to com.mysql.jdbc.Driver
- Fixed error initializing an empty MySQL shared database when using a recent version of MySQL Java connector
- Fixed issue whereby a user specified Postgres jdbc jar was ignored
- Fixed issue when using Postgres version 9 or greater that was not deleting disk files containing data for large documents that were deleted from the database, allowing orphaned files to accumulate in the user's directory. These files will now be deleted in the background when Geneious Prime is running
- Fixed problem scheduling background cleanup processes when MySQL or SQL Server database is in different timezone than Geneious client
- Fixed crash and/or hang when changing Geneious data location sometimes while connected to a shared database
Geneious Server:
- Fixed problem running jobs submitted by Geneious Prime on Linux when the user home directory is network shared with the computing cluster
Patch 2020.2.1 (14 July 2020)
- Alignment View: Fixed partial CDS extraction producing a sequence with a frame shifted translation
- Analyze CRISPR Editing Results: Fixed crash on some data sets and improved handling of Sanger data
- Batch Restriction Cloning Workflow: Workflow updated to use the modern restriction cloning operation
- Find in Document: Fixed so that it works on "Text View" and is not wrongly disabled sometimes on "Annotations" view
- Genbank Export: Moved option to include restriction sites as features to Advanced Preference
- Genbank Import: Prevent importing of invalid primer annotations
- Import BLAST XML: Fixed crash when importing BLAST results from XML files when BLAST services are disabled in geneious.properties
- Optimize Codons and Analyze Silent Mutations: Reverse selection is now indicated in the options (when selecting from right to left)
- Primer Design: Generated primers use appropriate IUPAC ambiguity code instead of N
- Restriction Enzymes: Prevent crash during Geneious startup when an invalid enzyme file is being loaded
- Search:
- Creating a new database in a new directory correctly resets recently viewed items in search popup
- Clearing search history in general preferences resets recently viewed items in search popup
- Fixed errors with non-alphanumeric characters in the search query
- Fixed UI rendering issue when searching multiple shared databases
- Improved result sorting
Patch 2020.2.2 (23 July 2020)
- Shared Database: Fixed compatibility issue when using PostgreSQL version 9 or greater that could result in data loss (Affected Geneious Prime 2020.2.0 and 2020.2.1)
Patch 2020.2.3 (19 August 2020)
- Find in Document: Fixed long freeze when opening dialog
- General: Fixed slow initialization of local folders when there are thousands of folders
- Search: Fixed crash on shared database when query is a double quotation mark
- Search: Fixed queries containing special symbol not finding some documents
- Search: Improved speed for finding documents shown in the document table
Patch 2020.2.4 (17 September 2020)
- Licensing: Improved ability to use renewed licenses without changing the license key
- Shared Database: Fixed a bug preventing some users from connecting with windows authentication
- Shared Database: Fixed CSV metadata import not working when importing directly into a shared database
Patch 2020.2.5 (8 December 2020)
- Operating System: Fixed crash when Geneious is hanging on MacOS Big Sur
Version 2020.1 (11 February 2020)
Patch Versions:
2020.1.1
2020.1.2
Features:
- Import metadata onto sequences and other documents from columns in a CSV/TSV format spreadsheet
- Improved automatic annotation of plasmids and other sequences
- Option to only annotate the best matching feature of a type at each location. If this option is
selected
only
the annotation with highest similarity will be found at each location based on a specified overlap length
- New database of standard plasmid features for use with Annotate from Database, with extended feature
set,
better conformation to GenBank annotation types and colouring of annotations for colored reporters that
match
the reporter colour
- Pairwise alignment between query and reference now included on annotations for each match found using Annotate from Database
- Addition of a 'Reference Features' folder as the default Source for Annotate from Database, to which
additional folders with custom features can be added alongside the provided features
- Codon Optimization and Back Translation improvements
- Avoid defined short sequence motifs (as for RE sites), using a modification of the dynamic
programming
algorithm described in Condon
and Thachuck (2012)
- Generate multiple optimized versions of a sequence simultaneously, co-optimising to increase the
pairwise
distance between them
- Restriction enzymes to avoid in the optimized result can now be fine-tuned by selecting a subset of the
chosen
enzyme set
- List of codon usage tables included with Geneious reduced to only show high expression tables
- Option to choose between producing different sequences or reproduce results when operation is re-run
(default
is to produce a different sequence each time)
- Automatic primer specificity testing when running Test with Saved Primers to identify any additional
'Off-target' binding sites primers found on the sequence. Off-target information for the tested document will be
added to the new primer annotations.
Minor Features:
- Restriction Cloning: Option to specify a subset of enzymes to use from the selected enzyme set
- Batch Rename sequences based on the name of an annotation that is present on the sequence
Plugin Development:
- Wrapper Plugin system now supports:
- de novo assemblers
- Running Linux programs under the Windows Linux Subsystem
- Wrapper Plugins - UI improvements:
- Can now add a checkbox in the options boxed section heading
- Added 'fill horizontal space' setting for allowing more flexibility in the user options layout
- Added ability to specify a command line option for checkboxes which are unchecked
- Can now add user options that are split into different sections on the command line
- Wrapper Plugin system - other improvements:
- Map to reference includes stdout & stderr in the assembly report if the 'Save standard out' option is on
- Added variable for number of CPUs on the machine it is being run on
- Added option for attaching TSV/CSV metadata to sequences produced by the plugin
- Documents generated by SequenceAnnotationGenerators are now assigned unique names when they're added to a local
database folder
- Fixed various sequence copying methods to include all displayable fields on the created copy
Fixes and Minor Changes:
- Document Table: Now considers spaces when sorting documents
- History View: Entries can now be selected for copy-paste
- History View: Show the fields within each history entry in a fixed order instead of random order
- Sequence Assembly: Assembly reports are now saved by default
- Alignment View: Highlighting is now on by default for pairwise alignments
- Batch Rename: Added a warning to the preview panel indicating that the action cannot be undone
- Restriction Enzymes: Default enzyme sets included with Geneious now update automatically on first launch
- Virtual Gel: Fixed crash when enzymes have unknown cut sites
- Cloning UI: Fixed bug where the sequence was deselected when changing enzymes or making other changes in the
construct layout view
- Cloning UI: Fixed bug where annotations table would sometimes show up below the sequence preview in the cloning
options
- Codon Optimization: Fixed a bug where users could accidentally select the dividing line between custom and
bundled codon usage tables
- Workflows: 'Group Sequences By Name' workflow now works on protein sequences
- Workflows: When a workflow exposes an option which is not applicable to the selected documents, Geneious now
fails to run with an informative message instead of crashing
- Workflows: Fixed crash on startup after external file synchronization software has created extra files in your
database when detecting conflicts
- Contig Assembly: When assembling by name, if all sequences within sequence lists have identical values for a
particular field then that value is now copied to resulting contig assemblies
- Map to Reference and de novo Assembly: CPU usage now excluded from assembly report for non-Geneious algorithms,
as the value reported was incorrect
- SPAdes Assembler: Fixed canceling under Windows to actually stop the SPAdes program
- Export: Truncate long document names automatically instead of failing to export
- Export: Improved export to Geneious format to fail gracefully rather than creating an invalid Geneious file
when there is a problem loading documents referenced by the document being exported
- Export: SAM/BAM export uses sample name instead of document name as read group sample name field
- Import/Export: BED format now accommodates undirected annotations (previously undirected annotations were
treated as forward directed annotations)
- Import: Fixed SAM/BAM import failure when importing a large file which contain a read with a name over 255
characters long
- Import: SAM/BAM import will now fail with an appropriate message instead of crashing when SAM/BAM file is
corrupt
- Sequence View: Display primer extensions that go beyond the end of the sequence
- Sequence View: Fixed bug where repeat finder annotation links to other locations in the sequence didn't work if
the sequence name contained a colon
- Sequence View: Fixed the chromosome selector so that it doesn't truncate long sequence names when showing the
drop down list
- Sequence Extraction: Fixed a bug where "Extract Digestion Fragment" could crash for restriction sites located
right at the origin
- Test with Saved Primers: Increased size of number input fields on Linux and MacOS
- Primer Characteristics: Fixed crash when trying to calculate characteristics for sequences with very high
degeneracy
- Primer Design: "Design for Sequencing" no longer incorrectly generates paired primers
- Local Documents: Fixed occasional crash that could happen at any time during background indexing
- General: Fixed crash which occurred sometimes after pasting undisplayable text into input dialogs
- Sequencing Profiles: Fixed crash when drag’n’drop importing an exported profile
- Linux UI: GTK version 3 is now used if available, on Linux distributions other than Ubuntu
- Shared Database: Non-shared workflows are no longer stored in shared databases
- Shared Database: Read-only folder status is now updated correctly when changed (previously required restart for
some changes to show in UI)
- Shared Database: The delete, rename, change folder color actions enabled state now accurately reflects folder
permissions
- Shared Database: Prevent adding new user accounts with duplicate names
- Shared Database: Fixed bug whereby new user accounts were created in Geneious when the Username was typed with
different capitalization or spaces at the front and end
- Shared Database: Fixed poor performance connecting to a shared database which had hundreds of workflows
Other Notes:
- An email address is now required for account management purposes and to make sure we can contact you with
important updates
- Java Version: Update bundled JRE to 11.0.6 for macOS
Patch 2020.1.1 (10 March 2020)
- Improvements to the SnapGene *.dna File Importer:
- Restriction enzymes can now be imported as annotations, as an Enzyme Set, or ignored
- Restriction enzymes are now imported only from documents containing custom enzyme sets
- CDS annotations with introns are now imported correctly
- Primers with mismatches and extensions are now imported correctly
- Fixed a bug where primers with multiple potential binding sites weren't always annotated in the best position
- Fixed bug where linear sequences were sometimes imported as circular
- Fixed bug where db_xref qualifiers on annotations weren't imported
- Metadata Import: Now ignores leading and trailing space characters in spreadsheet data when matching with document field
- Metadata Import: Made various small UI improvements
- Restriction Cloning: Fixed a crash running with a non-default enzyme set and certain advanced enzyme chooser options
- Restriction Cloning: Fixed a bug where the incorrect enzyme set could sometimes be displayed in the advanced enzyme chooser
- Restriction Cloning, Codon Optimization, and "Find non-cutting enzymes" now remember the selected enzymes that were used previously
- Annotate from Database: Removed several redundant features from the Geneious Plasmid Features folder
- Annotate from Database: Fixed crash when target sequence has non-cutting enzymes recorded on it
- Test with Saved Primers: Added dialog to report on any additional binding sites found when specificity checking primers to be annotated
- Primer Pairs: Fixed a crash which occurred sometimes when Pair Selected Primers was run on primers in an alignment
- Alignment: Fixed crash when selecting sequence lists which contain no sequences
- Sequence Search: Fixed bug which could lead to results missing from query centric alignment view in rare cases
- Clustal Omega: Fixed 'Preserve input sequence order' option not working correctly when there are identical input
sequences
- RNA/DNA Fold View: Fixed a bug where the default energy model was used instead of the specified model
- Shared Database: Usernames with spaces now display properly in dialogs
- Sassafras Licenses: Fixed misleading error message when connection is lost to Sassafras KeyServer
- General: Fixed occasional hang on shutdown
- Windows HiDPI: Fixed tooltips missing the last few letters, words, or entire line sometimes
- Windows Java Version: Reverted bundled JRE on Windows from 11.0.6 (in version 2020.1.0) to 11.0.4 to prevent
crash during startup when the system is set to use some non-english languages
Patch 2020.1.2 (07 April 2020)
- Restriction Cloning: Fixed a crash creating or running workflows with a fixed vector
- Map to reference: Fixed crash sometimes when mapping contigs to a reference sequence
- Map to reference: Fixed read names sometimes having "extraction" appended to them when mapping a contig to a
reference sequence
- SAM/BAM Importer: Fixed crash when importing some SAM/BAM files where one or more referenced sequences have
identical names to a sequence list in the folder
- SnapGene Import: Fixed crash importing some annotation qualifiers
- Optimize Codons: Ambiguous bases in custom forbidden motifs are now handled
- SnapGene Importer: Fixed rare bug where sometimes enzymes in a custom enzyme set weren't all annotated
- Shared database: Fixed crash connecting to shared database as a different database account from the one you have
previously connected as when there is a shared workflow in the database owned by one of these accounts
- Restriction Enzymes: Prevent crash during shutdown when enzymes from inaccessible documents are being accessed
- Metadata Import: Fix overwrite warning when importing data onto empty document description fields
Version 2020.0 (8 October 2019)
Patch Versions:
2020.0.1
2020.0.2
2020.0.3
2020.0.4
2020.0.5
Features:
- Clustal Omega replaces ClustalW aligner giving greater scalability and improved alignment quality
- Improved Back Translation and Codon Optimization
- Can now use the codon usage table as a target distribution to optimise all codons (rather than just rare ones) using codons selected randomly weighted by frequency
- Choose to optimize the selected region of a sequence or the full sequence
- Use the codon optimisation algorithm for un-ambiguous Back Translation of a protein sequence
- Improved Annotation of CDS features from a reference Database
- Automatically adjust single-interval CDS annotation boundaries to match the nearest ORF
- Gene annotations that exactly match CDS annotations are also adjusted when transferred together with a CDS
Minor Features:
- Primer characteristics
- Now calculated for the full primer rather than just the binding region
- Tm for primers longer than 60 bp is now calculated, using the Chester and Marshak “Rough Tm” algorithm
- Text View: Save and share custom format settings as Options Profiles
- Folder Path: New option to show the name and path of the currently selected folder in status bar, with clickable links to any folder in the path (breadcrumbs)
- New “Stop codons” color scheme in the Sequence View for protein sequences and translations
- Consensus Calling:
- “Call Sanger Heterozygotes” setting is now available on alignments containing Sanger sequences as well as contigs
- Introduced a new “Highest Quality (Raw)” setting which does not apply various heuristics used to improve the accuracy of quality scores for “Highest Quality (Adjusted)”
- Renamed “Highest Quality” to “Highest Quality (Adjusted)”
- Spreadsheet Importer: Add “Notes” as a field that can be imported
- Easter Egg: See if you can find the option to view animated chromatograms :)
Plugin Development:
- Improved wrapper plugin system allows more flexible custom plugin creation
- Added support for creating wrapper plugins for “Map to Reference” operations
- Now allows dependencies between options which disable other options
- New layout options such as boxed sections, advanced options, and multiple options in the same horizontal row
Fixes and Minor Changes:
- GenBank Exporter: Added an option to re-translate CDS/ORF annotations that are truncated, rather than using the original annotated translation property
- Annotation Table: Renamed the “Translation” column to “Annotated translation”
- Annotation Table: Values for multiple qualifiers with the same name will now be shown as a semicolon-delimited list
- Convert to Oligo: Added constraints preventing conversion of sequences longer than 400 bp or circular sequences into primers or probes
- Sequence Extraction: Annotations are now explicitly truncated to the bounds of the extracted region
- Sequence Extraction: Fixed sometimes incorrect codon start property when extracting a partial reverse-directed CDS or reverse complement of a forward-directed CDS
- Sequence View: Selections on big sequence lists where every sequence is shown separately are now associated with the correct sequence and aren’t kept when switching to other sequences in the list
- Sequencing Primers: Prevent crash when allowing degeneracies
- Gibson Cloning: Fixed crash when starting Gibson with only sequence lists selected
- NCBI WGS Sequences: Fixed summary documents to show the number of contigs to download instead of incorrectly displaying sequence length in this field
- VNTI Import: Fixed a bug where annotations that are crossing the origin weren’t propagated correctly
- Workflows: Fixed paired read status being lost on sequence lists when running some operations which produce annotations
- Map to reference: Fixed rare crash when mapping to repetitive region with indels
- SAM/BAM Import: Fix crash importing multiple files when one has no reads
- SAM/BAM Import: Fixed rare crash when importing some SAM/BAM files
- Shared Database: Fixed an issue preventing being able to view a folder with a large number of documents in a SQL Server shared database
Other Notes:
- Support for 32-bit Windows has been discontinued from Geneious Prime 2020 onwards
Patch 2020.0.1 (beta) (29 October 2019)
- Sequence Alignment: Clustal Omega now supports multiple threads on Mac OS
- Annotate from Database: If a CDS cannot be adjusted to match the nearest ORF it will now still be transferred, whereas in the first beta invalid CDS annotations were not transferred at all if they could not be adjusted within the specified similarity threshold
- Annotate from Database: Fixed a crash that could sometimes occur as the operation finished
- SAM/BAM Importer: If all reads do not map to the reference sequence(s), Geneious now imports those as unmapped reads rather than importing nothing
- Back Translation: Replaced the EMBOSS-based operation with a more flexible operation
- Codon Optimization: When optimizing rare codons only, replacement codons are now chosen randomly in proportion to their fraction value in the codon usage table
- Printing: Fixed bug where in some situations it would print infinite pages
- GenBank Exporter: Users will no longer receive a warning that CDS translation qualifiers won’t be used when they’ve explicitly requested that new translations be generated for truncated annotations
- Import from Clipboard: Fixed failure to import CSV/TSV files which start with a field called “Sequence”
- NCBI: Fixed crash viewing and downloading full TLS sequences
- Primer Characteristics: Clearer display of characteristics for primers with or without extensions
- Primer Characteristics: Fixed bug when calculating product size for primers that span the origin
- Sequence Viewer Statistics: Fixed translation statistics for selections spanning the origin on circular sequences
- Sequence Viewer Statistics: Fixed a bug where molecular weight was incorrect for regions spanning the origin on circular sequences
- Shared Databases: Improved performance to load documents in a folder for MS SQL databases
- VCF Import: Fixed bug causing annotations to sometimes be lost during import
Patch 2020.0.2 (5 November 2019)
- First full release of Geneious Prime 2020
Patch 2020.0.3 (7 November 2019)
- Fixed problem installing FlexNet that affected new users on macOS
- Fixed a bug copying protein sequences with CDS annotations (also fixes similar bugs exporting in GenBank/GenPept format and displaying in the Text View)
Patch 2020.0.4 (3 December 2019)
- Licensing: Fixed FlexNet problems with new installation of Geneious Prime 2020.0.2 on macOS
- Annotate from Database: fixed crash that could occur when transferring certain annotations onto protein documents
- SAM Importer / Minimap2: Fixed importing SAM files which don't store nucleotides for secondary alignments so
that it uses the nucleotides from the primary alignment instead of all Ns
- SPAdes assembler: Fixed failing to run on data sets which have paired reads with spaces in their name
- Genbank Exporter: Fixed a bug where truncated undirected CDS annotations could cause the exporter to crash if
"generate new translation qualifiers" was checked
- Restriction Enzymes: Updated bundled enzyme set to prevent a crash in Golden Gate due to an outdated enzyme
- Workflows: filter operation now compares text fields which contain numerical values numerically rather than alphabetically
- Workflows: prevent batch renaming non-editable fields which could lead to crashes later
- Assembly: Fixed crash in rare cases
- Map to Reference: Added help entry for the advantages of using Minimap 2 over other mappers
- Development Kit: Removed 32bit configurations and updated setup instructions
Patch 2020.0.5 (14 January 2020)
- Uniprot: Fixed breaking change in the EMBL file format
- Annotate from database: Fixed bug where it was sometimes using the wrong genetic code when applying adjustments
to CDS boundaries
- GenBank Exporter: Improved speed of export for sequences that don't have the "Molecule Type" document field set
correctly (affects Mauve Viewer performance)
- NCBI Blast: Show GI number (Id) as the name and Description of a Hit if the accession isn't available
Version 2019.2 (21 May 2019)
Patch Versions:
2019.2.1
2019.2.2
2019.2.3
Features:
- Automatically Design Primers for tiled Sanger Sequencing
- Vector NTI Database Import:
- Added new Vector NTI Express Database importer (beta)
- Vector NTI databases can now be imported by drag and drop
- Various improvements and optimisations for a smoother import experience
- Improved Text View formatting of Sequences and Alignments:
- Support formatting and export of sequences in accordance with U.S. Patent Office requirements
- Can now format sequences into blocks of residues separated by gaps
- Specify regions of a sequence to translate
- Highlight regions of alignment with grey background, based on comparison to reference sequence
Minor Features:
- Primer Characteristics:
- Manually pair primers together in the Sequence View to link and calculate pair dimer Tm and product size
- Calculate characteristics for primer binding regions up to 60 bp when testing, importing or manually adding primers (previous limit 36 bp)
- Annotate from Database:
- Sequences without annotations in the database can optionally be used to annotate the query sequence as misc_feature annotations
- The maximum length of merged annotation names is now limited to 1000 characters
- 'Map reads to reference sequence by name' workflow now supports multiple sets of reads per reference sequence
- Find in Sequence: Adjacent occurrences of single character selections can now be individually replaced, allowing single character 'find and replace' functionality on short sequences (under 10 kb)
- Document Chooser: Added button to jump to the folder that is currently selected in the main window
- De novo Assembly:
- Automatically trims paired reads which extend back past the start of the other read. This happens when the amplified region is shorter than the read length
- "Don't merge variants with coverage over..." improved for high coverage areas by merging variants when the minor variant has under 10% of the coverage of the major variant
- Easier Shared Database Rollout:
- A connection in Geneious Prime can now be pre-configured by an admin, using the geneious.properties file
- Microsoft JDBC Driver for SQL Server is now bundled with Geneious Prime as the default driver for Microsoft SQL Server
Fixes and Minor Changes:
- SPAdes Assembler: Updated to version 3.13.0
- Vector NTI Database Import: A new folder is created for each VNTI database that is imported into Geneious (previously databases were merged)
- Vector NTI Database Import: Oligos over 36 bp are now annotated with a Binding Region
- Vector NTI Database Import: Now asks for import location when no folder is selected on import (previously database was not imported)
- Contig View: Added a "Remember my preference" checkbox for editing circular-mapped contigs as linear alignments
- Alignment View: Annotations in tracks on the consensus will now update to reflect edits made to the consensus
- Alignment View: Consensus numbering is no longer shown when numbering "All Sequences" if the consensus is not visible
- Sequence View: Improved layout of annotation labels
- Sequence View: When adding annotations to multiple sequences in a list by selecting a range past the end of some circular sequences, annotation intervals are now adjusted to account for circularity
- Sequence View: Fixed crash sometimes when editing circular sequences
- Sequence View: Fixed a crash when opening high-coverage contigs
- Sequence View: Fixed a crash when unchecking "Show Annotations" with an annotation selected
- Text View: When viewing an alignment, changes to the consensus in the Alignment View take effect immediately when switching to Text View
- Text View: Fixed a crash viewing PDB documents with model serial numbers longer than two digits
- Text View: Fixed a hang when viewing assemblies
- Consensus Calling: Fixed incorrect consensus calling on the ends of chromatograms which have been hard trimmed
- Expression Analysis: Volcano plot p-values equal to 0 are now clipped to slightly less than the smallest nonzero p-value
- Expression Analysis: Vertical lines denoting outliers on volcano plots are no longer shown outside the plot region
- Expression Analysis: Fixed color buttons in volcano plot options on Mac OS
- Trim Primers: Increased maximum number of degenerate bases allowed in a primer
- Trim Primers: Fixed bug where if the same primer was on both ends of a sequence (due to mispriming) it would only be trimmed from one end
- Extract PCR Product: Prevent hang extracting PCR products from assembly documents
- Sequence Extraction: Fixed a crash extracting PCR products or restriction fragments from sequence lists containing a single sequence
- Document Table: Fixed a crash that could sometimes occur when performing certain actions (e.g., paste) after deleting a document
- BLAST: Fixed a crash running BLAST with selected annotations on an alignment consensus
- BLAST/NCBI: Fixed a crash running BLAST or NCBI searches that take a very long time
- Workflows: Improved performance when deleting lots of workflows
- Progress messages: Fixed truncated percent complete message in some progress windows
- Preferences: Fixed crash in rare situations when changing data location
- Update Check: Fixed crash when checking for updates that prevents Geneious from starting due to an unauthenticated proxy server
- Public API: Added a class DatabaseFolderImporter to support importing folder structure along with documents
- Java Version: Updated Java to 11.0.3
Patch 2019.2.1 (18 June 2019)
- Text View: Changes to the Custom formatting options now take effect immediately
- Text View: Fixed a crash displaying alignments with non-default highlighting options when highlighting is disabled
- Sequence View: Annotation labels displayed outside annotations are now darker for very light annotation colours
- Sequence View: Added an advanced preference "SequenceViewer.AnnotationTextMaxLuminosity" to force external annotation labels to be drawn in darker colours
- Sequence View: Fixed crash displaying the "add primer" button
- Vector NTI Import: Added a message indicating that the VNTI Express importer is beta functionality
- Public API: Fixed a bug preventing the ability to make collapsible Options conditionally visible
- Primers: Geneious now warns the user if the Design for Sequencing primer operation has hung due to Primer3
- Primers: Geneious now filters out invalid primers which may arise when running the Design for Sequencing primer operation
- Primers: Tm results are now rounded up to 0 if a negative result is returned by Ntthal (Primer3)
- Primers: Geneious now wares the user if any primers in the set could not be designed when running the Design for Sequencing primer operation
Geneious Server and Geneious Server Database:
- Allow upgrade when SELinux is in Permissive mode instead of Disabled
Patch 2019.2.2 (9 July 2019)
- Licensing: Provided compatibility with new versions of Geneious Floating License Manager
- Vector NTI Import: Enabled drag-and-drop import for VNTI Express Designer databases
- Text View: Improved performance for large sequence lists
- Text View: Fixed a bug where copying rich text alignments/sequences failed to provide formatting on Windows
- Text View: Fixed number positioning for alignments formatted with space-delimited residue blocks
- Sequence View: Fixed a crash unchecking "show annotations" with a primer selected
- Sequence View: Fixed a crash laying out restriction site names when cutsite locations are not shown
Patch 2019.2.3 (24 September 2019)
- MacOS Compatibility: Added support for running on macOS 10.15 (Catalina) - More information
- ClustalW: No longer supported on Mac OS 10.15 (Catalina)
- Vector NTI Import: Added support for importing lineage for protein documents translated from DNA documents, when importing VNTI archive files and VNTI Advance databases (also supported for VNTI Express databases)
- Vector NTI Import: Calculation of primer characteristics is now optional, to reduce import time
- Vector NTI Import: VNTI Express database import now continues to import, and gives a warning, when invalid annotations are present on circular sequences
- Vector NTI Import: No longer importing potentially incorrect annotations from VNTI display settings
- Vector NTI Express Import: Fixed a bug where annotations could unexpectedly appear when propagating changes from DNA documents to protein descendents
- Primer Operations: Primers over 36 bp are now annotated without characteristics in 32-bit Geneious on Windows, as a Primer3 crash calculating the characteristics causes a failure to annotate primers
- Restriction Enzymes: Fix a bug where changes using a custom modified enzyme could not be propagated
- Codon Optimization: Fixed a bug where restriction site annotations were removed in the result document if they weren't unique
- Sequence Extraction: Fixed bug where annotation intervals were concatenated in the wrong order when extracting the reverse complement of a reverse-directed multiple interval annotation from a circular sequence
- BBDuk: Fixed problem with fastq quality coding in trimming results
- RNAfold: Update to version 2.14.3 of Vienna RNAfold
- NCBI Services: Removed NCBI's SNPs service after NCBI made breaking API changes
- Public API: Added an interface to allow GeneiousGridDocumentOperation instances to register a LocationChangedListener to allow options to be visible/enabled dependent on whether the operation is run locally or remotely
- Licensing: Updated FlexNet Publisher to version 11.16.3
Version 2019.1 (19 February 2019)
Patch Versions:
2019.1.1
2019.1.2
2019.1.3
Features:
- Customizable Text View:
- Sequence layout can be formatted to alter wrapping, numbering, sequence color and presence of reverse complement and translation
- Alignment layout can be formatted to alter numbering, sequence color and highlighting of agreements/disagreements to consensus
- Genbank format available for all sequences (2019.1.1)
- Full sequences can be copied to the clipboard as plain or rich text, or saved as a plain text document (2019.1.1)
- Primer Design Improvements:
- Primer specificity automatically tested within the template sequence when designing primers, and presence of any additional binding sites recorded on the primer annotation
- Option to control the minimum distance between primers designed on the same strand - defaults to minimizing creation of duplicate primers when multiple primer pairs are designed together
- Annealed Oligo Cloning: Added workflow to create a sequence with annotated overhangs representing the sticky ends created by annealing two partially overlapping oligos
- Restriction Enzymes: Methylation sensitivity information shown in tooltip when mousing over a restriction enzyme
Usability Improvements:
- Extract PCR Product: Now uses the primers selected in the Sequence View by default, if one or two opposite-facing primers are selected
- Document chooser: Added checkboxes for selecting multiple documents when choosing documents such as primers or reference sequences
- Find Variations/SNPs: Allows alternative type names (e.g., 'misc feature' instead of 'misc_feature') when restricting regions where variants will be annotated
- Set Paired Reads: Pairing by name supports reads that differ in the name by H/K (for heavy/kappa chain pairs)
- Set Paired Reads: Pairing by name supports reads when the variable character is anywhere within the name rather than just towards the end of the name
- Sequence View: Added 'Error Free Odds' to Sequence View Statistics, indicating the probability the selected sequence/region contain no sequencing errors
- Consensus Calling: Added setting (default on) to analyze contributing sanger traces for heterozygotes and reflect that in the consensus sequence
Fixes and Minor Changes:
- BLAST: Alternative BLAST services can now specify login information
- Test with Saved Primers: Now supports multiple selected regions on one or more sequences
- Test with Saved Primers: Added note explaining that mismatches are not considered when calculating Tm
- Sequence View: DNA Probe Bind annotations are now displayed above the sequence by default
- Sequence View: When selecting an annotation, selection tooltip now appears next to annotation rather than next to the mouse cursor
- Sequence Editing: Manually edited positions are assigned quality scores of 63, which is higher than any Sanger quality scores. Consensus calling heterozygote analysis is skipped on bases with quality score 63.
- BBTools: Updated to version 38.37
- Genbank Export: Updated valid Genbank feature qualifiers
- Genbank Import: Sequences exported from NCBI as INSDSeq XML files can be imported even though they are missing the standard XML declarations
- Silent Mutation Analysis: Fixed a bug where first codon in later intervals could be interpreted as a start codon
- Extract PCR Product: Only creates active links when the corresponding option is checked
- Test with Saved Primers: Fixed crash testing primers that amplify a region on a circular sequence spanning the origin when multiple sequences are selected
- Primer Operations: Add a link to the Primer3 website
- Sequence View: Fixed crash after deleting annotations when viewing a sequence in multiple windows
- Sequence View: Fixed crash running annotation generators on some sequences with restriction sites after deleting annotations in a separate viewer
- BLAST: Fixed hang sometimes when deleting blast results
- Find CRISPR Sites: Fixed crash that would occur when scoring CRISPR sites against a database that only contains protein sequences
- Alignment View: Fixed poor performance or hangs when viewing translations on some large alignments
- Tree View: Fixed a couple of crashes that could occur when working with trees with great depth
- Restriction Analysis: Fixed crash when creating a new enzyme set from separate sequence view window
- SnapGene Import: Fixed crash importing annotations with no name
- General: Fixed Geneious failing to let you use your Geneious data location sometimes due to file synchronization software
- General: Geneious now fails gracefully instead of crashing in some cases when some unknown file synchronization software creates synchronization conflict files in your Geneious database
- General: Fixed potential bug that causes Geneious to run as if it was invoked from a script while it actually wasn't
Plugin Development:
- Plugin Development: Shows a warning if a plugin developer doesn't provide an email address that bug reports can be sent to
- Public API: Layout-dependent options can be added to options without labels
- Public API: An enumerated document field may have its list of possible values changed. All existing documents and new documents with this field will show the new possible values after a new document is generated and restarting Geneious
Geneious Server and Geneious Server Database:
- Add configuration file for customer use for access logging feature
- Fix warnings in logs about trying to decrement references when there are none
- Fix connection to Geneious Server made through shared database dialog not respecting required Linux user and group settings
Patch 2019.1.1 (5 March 2019)
- Text View: Added option "Save as *.txt" to export the full sequence as a plain text file using the current display settings
- Text View: Added option to copy full sequence to clipboard in plain and rich text
- Text View: GenBank format available for all individual sequences and up to 10 concurrently selected sequences
- Text View: Added Display Options for GenBank format
- Text View: Improvements to the toolbar and Display Options UI
- Text View: Added option to display sequences without reformatting, for example to show NCBI Gene record information in the Text View (displays sequence as in version 2019.0 and earlier)
- Text View: For alignments, the consensus sequence generated by Geneious is used, rather than a new one created by ShowAlign
- Text View: Fixed reverse translation frames to behave consistently with the sequence view
- Text View: Fixed crash when viewing empty sequence lists
- Primer Design: Added ability to find Off-target sites with mismatches to the primer
- Primer Design: Show information dialog when Off-target sites are found during a run of Design New Primers
- Primer Design: Added sequence name to Off-target site location in annotation properties
- Primer Design: Added "Off-target template" annotation qualifier, which specifies the sequence that the primer was checked against to give the number of off-target binding sites
- Primer Design: Information about Off-targets is now removed from primers when they are extracted from a sequence
- Primer Design: Display the column for "# Off-target" Sites in the annotation table for primers
- Primer Design: Fixed bug where Off-target information was not given for all primers
- Primer Design: Fixed bug where primers designed over gaps reported the target binding site as Off-target
- Primer Design: Fixed bug where the Minimum Primer Distance setting was always selected
- Icons: Fixed oversized info icon when viewers are hidden
- Nexus Exporter: No longer adds single quotes around sequence names with digits
- Plugin Development: Fixed a bug where options that were layout-dependent on Options.BooleanOptions with value-dependent options weren't added to the panel
Patch 2019.1.2 (9 April 2019)
Fixes and Minor Changes:
- Deleting Items: Fixed bug where files could not be moved to 'Deleted Items' after changing the database
- Deleting Items: Fixed wrong location of 'Deleted Items' in the Folder Hierarchy after changing the database
- Startup: Fixed crash on Windows 32 bit installations for some HiDPI settings
- Shared Database: Added advanced preference 'SharedDatabase.showUser' to display username next to database in the Sources Panel
- Text View: Fixed a crash viewing mixed nucleotide and protein sequence lists with only one sequence of either type
- Extract PCR Product or Digested Fragment: Fixed bug where the wrong sequence from a sequence list or alignment could be extracted
- Importing CSV Files: Importing CSV files no longer require each row to have the same number of columns
- Fix Geneious web links not working in Windows browsers
Patch 2019.1.3 (17 April 2019)
Fixes and Minor Changes:
- Shared Database: Fixed a bug where upgrading a local database would hang if connected to a shared database
- Startup: Fixed a crash on startup where the local database and server database plugins were not initialized in the correct order
- Genbank & VNTI Import: Genbank files produced by VNTI have an invalid 'COMMENTS' section that is now imported correctly into Geneious
Version 2019.0 (2 October 2018)
Patch Versions:
2019.0.1
2019.0.2
2019.0.3
2019.0.4
Features:
- Custom codon usage tables:
- Back translate and optimize codons using custom tables
- Import EMBOSS cusp format
- Import GCG CodonFrequency format. A public database of these can be found at https://www.kazusa.or.jp/codon/
- Create primers directly in the Sequence View more easily:
- Real-time display of length and melting point (Tm) when selecting short regions in the Sequence View
- Add a primer to the selected region of sequence easily, with new button added to the Sequence View
- Improved display of primers, including 5' extensions, in the Sequence View:
- Clear visualisation of primer extensions (tails), with proportional length
- Display of nucleotides in the extension region when zoomed in
- Display of primer extensions components (e.g. restriction sites, tags, spacers) as mini annotations on the primer extension
- Coloring of forward and reverse primer annotations based on direction in relation to sequence rather than annotation type
- Primers default to displaying above the sequence when showing forward strand only
- Easier annotation of existing primers onto sequences:
- Simplified "Test with Saved Primers" operation, for testing if any primers in Geneious match a target sequence
- New "Add Primers" operation for pasting in primers designed outside Geneious and annotating them on a target sequence immediately
- GenBank file export improvements (GenBank flat file format):
- Drag-and-drop export of sequences under 1Mb to the desktop and directly to some applications, in GenBank format using default settings
- Added option to export Meta-Data fields as GenBank structured comments
- More flexible options for converting annotation types and documents names to strict GenBank format, with improved options layout
- Improved Sequence View statistics:
- Added calculation of protein charge at pH 7.0, and updated the pKa values used for the Isoelectric point calculation on amino acid sequences
- Added counts for common amino acid groups on both amino acid and protein-coding nucleotide documents
- Added calculation of statistics for translation when viewing nucleotide sequences, including isoelectric point (pI), extinction coefficient and molecular weight
- Improved layout of statistics panel
- Extract a PCR product directly from Sequence View by shift-selecting a forward and reverse primer
- Extract a restriction digested fragment directly from the Sequence view by shift-selecting two restriction enzyme annotations
- Plugin management: Geneious can now be configured to offer a curated list of plugins and their updates via your internal network
Minor Features:
- Easier backbone selection for cloning operations:
- Now sets backbone by guessing which sequences is most suitable, rather than selecting the previously used backbone
- Use drag-and-drop to change the backbone in the Construct Layout View as well as inserts
- Added option to always use the leftmost sequence in Construct Layout View as the backbone
- Improved annotations table for primer documents for easier export of primers:
- New "Sequence (with extension)" and "Length (with extension)" columns for primers, turned on by default
- Tm, GC%, Hairpin Tm and Self Dimer Tm for primers turned on by default for primer documents
- The annotation type "primer_bind_reverse" is deprecated and no longer produced by operations in Geneious, use "primer_bind" with reverse direction instead
- Improved document naming:
- When extracting primers with manually set names, the primer name is not changed and the name of sequence the primer was extracted from is added to the primers description
- Output document name for some operations changed so that new document names start with the name of the original document (previously this was at the end)
- When assembling by name and saving in a sub folder, if the specified assembly name does not contain {Reads Name} then contigs are now named based on the batch name
- Batch Rename: Allow counter to start at an arbitrary value, rather than always starting at 1
- Show Folder Size: Right click on a folder in your local or shared database to calculate the size of that folder and all sub-folders
- Mask Alignment: Support NEXUS charsets including the "CHARSET name =" and final semi-colon in the NEXUS-style charset option
- Workflows: Drag-and-drop selected workflows to reorder list in "Manage Workflows" dialog
- Workflows: Added "Run workflow" option to menu, to easily run workflows that are not currently shown in the dropdown menu
- Set Paired Reads: Pairing by name supports reads that differ in the name by H/L (for heavy/light chain pairs)
- Set Paired Reads: Can now be run on stand alone sequences rather than just lists
- Vector NTI Database Import: Now generates a folder for each subset, so that your folders are organised the same in Geneious as they were in Vector NTI Advance
- Assembly Reports are now able to be exported in HTML
- Sequence View: Added an option to show translation based on annotations only
- Genetic Codes: Added "Amber Readthrough" genetic code
- Easter eggs: Added some interesting hidden features. See if you can find them :)
Fixes and Minor Changes:
- Restriction Sites methylation information is now automatically updated from rebase
- Find Restriction Sites: Changed default settings & restores preferences for various sequence types (smaller than 100kb)
- Find Restriction Sites: Added an option to turn restriction sites on or off from the General options tab in the Sequence View
- Cloning: Fixed bug where restriction sites were remembered from a previously set backbone
- Cloning: Fixed tag panel sizing to take scrollbar into account and made improvements for scaled displays
- Gibson Assembly: Fixed Gibson report reporting wrong set of bases being added via 'Gibson Primer Extension'
- Gateway Operations now find and handle slightly more diverse Gateway sites
- Primer Design: Characteristics for Selection now takes into account the direction of the selection
- Primer Extensions: Now preserves components of primer extension when extracting and annotating primers or editing the extension
- Primer Testing: Primers with identical binding sites, but different extension sequence, are no longer added as a single merged annotation
- Consensus Calling: Improved consensus calling around homopolymers in pairwise Sanger read assemblies
- Apply Variants: On variants without frequencies or allele counts, it uses the genotype property to determine ploidy
- Apply Variants: Can now run on variants without frequencies, allele counts, or genotype properties if the 'create ambiguities' setting is off
- Apply Variants: Fixed it wrongly generating ambiguities when the 'create ambiguities' setting is off
- Document History: For alignment and tree-building operations, the history now indicates which operation was used, rather than the category (e.g., "MUSCLE Alignment" instead of just "Alignment")
- Document searching: Can now search for all Text Document using Document Type advanced search
- Shared Database: Searchable fields list now updates when new documents are added
- Shared Database: Upgraded bundled copy of ojdbc used for connecting to Oracle databases to ojdbc8
- DNA/RNA Fold: Changed default temperature to 55 degrees
- Sequence Editing: Fixed bug where primer annotations were not removed from sequence in some situations when changes are made to the underlying sequence
- Sequence Extraction: Fixed bug when extracting the reverse complement of a forward-directed primer where the extension was downstream of the binding site in the result
- Viewers: DNA/RNA Fold hidden by default on everything other than oligos. New preference added to Appearance & Behaviour to change it back.
- Viewers: Dotplot (self) view hidden by default. New preference added to Appearance & Behaviour to change it back.
- Viewers: Lengths graph hidden by default on less than 20 sequences. New preference added to Appearance & Behaviour to change the threshold.
- Sequence View: When viewing circular sequences, the fit to screen button now moves to the origin of the sequence (in addition to fitting the zoom)
- Sequence View: Concatenation annotations are no longer shown by default, resetting the Sequence View options will hide them
- Sequence View: Removed redundant help button at top right of Sequence View
- Sequence View: Stylized DNA helix graph hidden by default. Can be turned back on under Customize Feature Set.
- Sequence View: GC Graph: AT line turned off by default
- Sequence View: Annotation labels are now centred within annotations
- Sequence View: Fixed poor performance when viewing thousands of sequences with tracks
- Sequence View: Fixed tracks occasionally turning off in circular overview when saving
- Sequence View: No longer asks whether to delete the underlying sequence when an annotation is deleted when editing is on
- Sequence View: Copying a selected primer annotation now copies the primer sequence, including extension and any mismatches
- Share button: Hidden by default. Can be turned back on under Customize Feature Set
- Alignment View: Numbering based on the consensus sequence is now disabled if the consensus is not visible
- Virtual Gel: This view is no longer available for contig assemblies
- GenBank Import: Handles line breaks in the LOCUS line (produced by e.g. VNTI Express)
- GenPept Import: Adds bonds that are nested in a join(bond(x),bond(y))
- GFF Import: Annotation intervals are now adjusted to match sequences from Fasta files with ENSEMBL-style headers
- GFF Import: Annotations missing the "ID" qualifier can now be imported as multi-interval annotations
- VNTI Import: Lineage for Gateway operations are created correctly even if no att-sites are specified in the VNTI enzymes
- SAM/BAM Import: Fixed crash importing soft trimmed reads when sequence data is not present on an alignment line in the input file
- GenBank Files: Fixed crash when a document has an incomplete comment from the annotation pipeline
- FastQ Import: Fixed crash importing paired files when there is a problem saving one of the files
- SnapGene Import: Fixed crash importing restriction sites from some sequences longer than 30,000 bases
- SnapGene Import: Improved handling of files with no sequence data
- Graph Export: Fixed crash when exporting graphs after deleting sequences without saving first
- Workflows: Limited number of workflows to show in the dropdown menu to 30 entries on macOS to avoid macOS bug that would cause Geneious to freeze
- Workflows: Convert to Oligo now keeps a copy of the original documents when run from Workflows in case a later step fails and they can't be recovered
- Wrapper Plugins: Fixed crash affecting annotation generators that run on alignments (e.g., FreeBayes) if reference sequence name contained no spaces or illegal characters
- Document Table: Fixed bug where it would sometimes not warn you when attempting to edit a non-editable field
- Licensing: Clarify menus and prevent problems regarding returns of borrowed floating licenses
- Backup data: Fixed a rare crash that could happen during backup as Geneious is shutting down
- SPAdes Assembler: Fixed bug that prevented the SPAdes assembler from running from workflows with custom kmer sizes
- Expression Analysis: Fixed crash when DESeq2 is run on sequence lists containing some sequences with no mapped reads for one or more condition
- Printing: Fixed crash when displaying the print preview at low zoom of the annotation table with lots of annotations
- Batch Rename: Renaming sequences no longer causes the sequence selector dropdown menu to disappear
- Custom BLAST setup: Fixed bug that caused continuous download of installer if the first try wasn't successful
- General: Replaced remaining uses of ftp links with equivalent http or https links
- General: Improved interface for choosing a destination folder
Geneious Server and Geneious Server Database:
- Fix inability of Geneious to cancel its jobs on a Slurm cluster when non-Geneious users of the cluster have submitted jobs with a syntax error in job name
- Replace use of hardcoded path /home/geneiousserver/tmp for server side temporary file storage with Java java.io.tmpdir
- Fix compatibility problems with Oracle database
Other Notes:
- Geneious renamed to Geneious Prime. For more details see Geneious Prime Rename
- Geneious Prime now comes bundled with Java 11 providing improved support for HiDPI screens.
Distributions for 32 bit Windows will continue to include Java 8 due to Java 11 being unsupported.
Patch 2019.0.1 (23 October 2018)
Fixes and Minor Changes:
- FASTA Importer: Fixed occasional crash that could occur importing FASTA alignments with non-ASCII characters
- Tree View: Fixed assignment of node values to branches on some Nexus trees
- Sequence Extraction: Removed "as annotated" reading frame option for translating aligned sequences
- Sequence Extraction: When extracting primer annotations with default names assigned by Geneious Prime (e.g., "1 F"), the original sequence name is now included in the name of the result document
- Cloning: Better indication about missing overhangs due to sequences that are too short for PCR
- Sequence View: Fixed crash viewing sequences with selected primers with extensions when primer annotations are invisible
- Drag-and-Drop Export: Now uses *.gb file extension and remembers previously used preferences
- Genbank Export: Settings now default to exporting annotations in non-strict format, maintaining long names (replacing spaces with underscore), and including metadata
- Primer Testing: Old Test with saved primers available to be run from workflows
- Primer Testing: Improved defaults, performance, and user interface for Test with Saved Primers
- Primer Testing: Added help for "Amplify/target selected region"
- Primer Testing: Improved "Amplify/target selected region" so that it finds primers that bind inside the selection if the value is > 0
- Annotation Table: Fixed crash viewing alignments with primer annotations on the consensus
- Document Import: Fixed a crash importing a document without selecting a folder that affected users who'd never imported anything or saved results
- Lineage: extraction of a region of a sequence from a list or alignment now shows the source sequence name in the lineage history
Geneious Server and Geneious Server Database:
- Fix crash on server that has no graphics card or integrated graphics hardware
Patch 2019.0.2 (30 October 2018)
Fixes and Minor Changes:
- General: Fixed progress bars in Windows 10 not showing a progress indication
- Trees: Fixed a crash that would happen when very large trees were exported in Nexus format
- Primer Testing: Renamed 'Add Primers...' to 'Add Primers to Sequence...'
- Primer Testing: Improved feedback about invalid options
- Primer Testing: Primers added using the "extract to folder" option from the "Add Primers to Sequence" tool no longer have the sequence name prepended to the primer document name
- CSV/TSV File Export: Previously exported fields are once again remembered
- Sequence View: Improved format and layout of statistics panel
- Sequence Extraction: Fixed a bug where extracting primers with context produced an oligo (primer) sequence with the extension (if present) in the wrong position
Patch 2019.0.3 (6 November 2018)
Fixes and Minor Changes:
- NCBI Databases: Modifying databases shows previously saved databases instead of always the default databases
- Nexus Exporter: Fixed handling of special characters in document fields (prevents tree building failures in some cases)
Patch 2019.0.4 (27 November 2018)
Fixes and Minor Changes:
- Annotation Table: Added advanced preference to show the 'Annotation Group' qualifier that was hidden since Geneious 11.1
- Gibson Cloning: Fixed a crash when no sequences are selected
- Sequence View and Primers: Fixed a crash when trying to show annotations on a primer extension
- Sequence View: Fixed crash copying primer annotations added using "Annotate from Database" without applying the annotations
- Sequence View: Fixed crash copying invalid primers
- Sequence View: Copying primer annotations from aligned regions containing gaps now creates an oligonucleotide sequence
- Licensing: Fixed problems activating FlexNet permanent licenses created for R12 and higher under old versioning scheme
- Fixed crash on startup when using x2go or certain other remote GUI access to the machine running Geneious Prime
- Plugin Development: Added a required VM option for running examples with Java 11 from IntelliJ or Eclipse
Geneious Server and Geneious Server Database:
- Geneious Server Database: Remove unnecessary login warning about lack of client or queue licenses
Version 11.1 (7 February 2018)
Patch Versions:
11.1.1
11.1.2
11.1.3
11.1.4
11.1.5
Features:
- SnapGene sequence file import (*.dna)
- Support for importing any mixture of files along with external reference sequences (SAM, BAM, GFF, BED, VCF)
- New CRISPR specificity scoring for guides with 5' PAMs, such as Cpf1 (uses a modified version of Zhang et al 2013)
- Concatenate Sequences or Alignments: Sequences can now be concatenated by index in input documents (instead of by name)
- BLAST: Multiple alternative BLAST services (NCBI BLAST Cloud, wwwBlast) can now be set up at the same time, allowing easy switching between them
- BLAST: Can now connect to NCBI BLAST Cloud servers (https://ncbi.github.io/blast-cloud/) and any other server supporting NCBI common URL API
- CSV/TSV export: Each sequence inside a sequence list can now be exported
Fixes and Minor Changes:
- Sequence View: Annotation filtering now fades instead of hiding non-matching annotations. Added option to hide them instead
- Sequence View: Selecting annotations or jumping to next annotation result using arrows or filtering briefly highlights that relevant annotation(s)
- Sequence View: Longer annotations are now generally positioned closer to the nucleotides than shorter annotations
- Sequence View: Fixed a rare crash when loading a new document while an editing action is in progress
- Sequence View: Prevented a hang loading sequences with large numbers of 0-length CDS and ORF annotations
- Sequence View: Behaviour of "Copy" and "Copy reverse complement" when selecting reverse-directed annotations is now consistent with sequence extraction
- Sequence View: Fixed incorrect inline translation when multiple annotations with codon_start qualifiers are selected
- Sequence View: Truncated annotation filter now matches annotations that appear truncated because they overhang the ends of the sequence
- Sequence View: Restriction enzyme cut sites ending after the last residue of a sequence are now rendered on the same line as the sequence in wrapped mode
- Sequence View: Paired primer annotations can now be overlaid on the sequence when zoomed out
- Sequence View: Fixed truncated annotations being drawn incorrectly when small
- Sequence View: Fixed crash when using 'save as image' while annotations table is empty
- Sequence View: Changed the default label position for annotations on circular sequences in order to reduce clutter
- Sequence View: Fixed bug where filter text would not fully apply if some text in the filter was selected and replaced by pasting from the clipboard
- Sequence View: Fix apparent hang after long keypress when MacOS is configured to show diacritic menu instead of repeating characters
- Sequence View Statistics: Change to a new rough Tm calculation formula that gives more accurate results
- Alignment View: Fixed crash or incorrect sequence data after sorting an alignment with a reference sequence, editing some sequences, and then saving
- Alignment View: When sorting aligned sequences, the first sequence will remain in place if it is set as the reference sequence
- Alignment View: Fixed crash in rare situations when deleting gaps from the end of an alignment
- Consensus Calling: Improved consensus calling around gaps in pairwise Sanger read assemblies
- Consensus Calling: Fixed bug where consensus sequence produced by assembly would sometimes not have quality information assigned when it should
- BBTools: Updated to version 37.64
- Go To Base: Fixed crash selecting sequence 0 on a sequence list viewing only one sequence
- Import: Fixed crash importing pairs of fastq files which each contain only a single sequence
- Import: Temporary files created when importing large files are now immediately deleted
- Import: Improve usability of dialog shown by multi-file import when there are files of unknown type
- Sequence Extraction: Fixed crash extracting regions consisting only of gaps from the leading or trailing ends of an alignment
- Sequence Extraction: Fixed crash extracting intervals from CDS annotations with invalid codon_start qualifier
- Extract Annotations: The include context setting on multi-interval annotations no longer includes the region between intervals more than once if the context would overlap or extend into other intervals
- Tree Building/NEXUS export: Fixed crash with very long taxon names
- Tree Building: Improved handling of illegal characters in taxon names
- Volcano Plots: Fixed crash loading documents with invalid Expression Difference annotations
- Text View: Fixed crash trying to view certain sets of multiple documents
- BLAST on Geneious Server: Puts result documents and Query Centric View into a subfolder
- NCBI: Downloaded WGS sequences get grouped into separate documents and reflect more closely the NCBI entry
- Gibson Assembly: Warns about invalid overhangs before running the operation
- Gibson Assembly and Golden Gate: Low-quality primer warnings are now displayed prior to completing the operation
- Local Documents: If a document was deleted shortly before Geneious was shut down, sometimes some of the data would not get completely deleted. On startup Geneious finishes deleting all partially deleted data now
- Shared Database: Prevent crash when trying to retrieve a document from cache if the database connection is interrupted
- Shared Database: Admin users can now rebuild the index of all documents in the database
- Shared Database: Fixed crash expanding 'More Options' in the search panel in databases with very few documents
- Document Searching: Annotations on the consensus sequence can now be searched
- Document Searching: Documents can now be queried for annotations by type or by name
- Annotate from Database: Conflicting codon_start qualifiers on otherwise similar CDS annotations will no longer be transferred to the result document
- Find Restriction Sites: 'Must cut between' and 'Must only cut between' now find enzymes with cut sites that overlap the given region
- Find Restriction Sites: Shows that a subset is selected whenever not all of the enzymes of that list are active
- GenBank Export: No longer loads all sequences into memory prior to export, which fixes excessive memory usage when exporting large data sets
- SPAdes: Fixed incorrect options for number of threads and memory when run on Geneious Server
- General: Geneious now fails gracefully instead of crashing in some cases when DropBox creates synchronization conflict files in your Geneious database
- Ligate Sequences/Concatenate Sequences or Alignments: Result document names now include input sequence/alignment names
- Gibson Assembly/Restriction/Golden Gate Cloning: Document names are now consistent with Ligate Sequences
- Golden Gate Cloning: Warns about conflicting internal cut sites if a primer is used to introduce a new site
- Restriction Cloning: Shows warning instead of crash when trying to propagate a change to a restriction site that was used in a previous restriction cloning experiment
- Administration: Can disable error reporting and social media sharing by editing geneious.properties in the Geneious install directory
- Administration: Allow system admin to hide access to local database to enforce all Geneious documents being stored on a shared database
Geneious Server and Geneious Server Database:
- Allow users to be de-registered from Geneious when the underlying authentication method cannot be modified e.g. when using LDAP
Plugin Development:
- Updated ExampleDocumentViewer to provide an example of using an external dependency
Patch 11.1.1 (27 February 2018)
Fixes and Minor Changes:
- Translate sequences: remembers setting whether to translate first codon as methionine or not
- NCBI: Increased request limit for some NCBI queries to 10 requests / second if an API key is specified
- NCBI: Fixed regression from 11.1.0 where gene documents may not be downloaded if they're on the same sequence as other genes
- NCBI Genes: Fixed 'Related Sequences' links in the text view
- File Import: Shows a list of all failed files if more than 10 files fail to import
- GFF Import: Fixed crash when importing grouped annotations
- Annotate from Database: Fixed crash annotating very short sequences
- Circular Sequence View: Fixed cursor on MacOS to rotate like it did prior to 11.1.0
- Map to reference: Fixed crash in some cases when discovering structural variants on circular reference sequences
- 16S Biodiversity: Fixed workflows bug that prevented batch analysis of multiple sequence lists
- Document Table: Fixed saving and loading of column order for folders with locked columns
- Installer: Fix msi upgrade install resulting in damaged bundled Java runtime
- Startup on Windows: Detect problems resulting from upgrading msi install using exe installer or vice versa
- CSV/TSV export: Include the sequence list name when exporting sequence lists
Patch 11.1.2 (6 March 2018)
Geneious Server and Geneious Server Database:
- Fix sporadic failures in Sun Grid Engine startup on standalone installation on CentOS 7
- Fix spurious warnings in log regarding failed attempts to download rebase enzyme updates
Patch 11.1.3 (10 April 2018)
Fixes and Minor Changes:
- GFF Importer: When importing embedded FastA protein sequence lists, short sequences are no longer misidentified as DNA
- NCBI Sequence Search: Fixed crash when a document doesn't specify a molecule type
- NCBI Sequence Search: Fixed rare crash when contigs don't have a 'join()' statement
- BLAST Query centric alignments: Multiple hits matching repeated regions are now distributed correctly across those repeats
- Tree Builder: Fixed rare crash that could occur when building trees out of alignment documents that referenced other documents
- Copy Translation: Now respects codon_start annotation properties
- Copy Translation: When copying multiple annotations, there is now an option to create a sequence list from the result or concatenate translated sequences
- Expression Analysis: Fixed crash when DESeq2 is run on sequences with CDS annotations added after mapping reads
- De Novo Assembly: Fixed crash in rare situations
- General: Allow admin to completely disable update checking
- Restriction Sites are associated with more accurate methylation information
- New Sequence: Now always auto-detects the sequence type
- Local Database: Added an option to rebuild the local database search index to the context (right-click) menu
Geneious Server and Geneious Server Database:
- Add ability to bulk upload user names via admin console when using network authentication such as LDAP
Patch 11.1.4 (1 May 2018)
Fixes and Minor Changes:
- BLAST Search: Fixed bug that causes a crash when creating a query-centric alignment in some situations
- GenBank Import/Export: Only replaces spaces in LOCUS names with underscore in strict mode & doesn't truncate long names in text view
- VNTI Import: Fixed hang when sequence data for documents with lineage is missing
- Workflows: It's now possible to move a block of workflows up or down in the "Manage Workflows" dialog
- Licensing: Upgrade FlexNet executables on Linux for compatibility with Ubuntu 18.04
Patch 11.1.5 (17 July 2018)
Fixes and Minor Changes:
- Tree/Alignment Distance Matrix View: Fixed bug that caused the labels to be out of order in some Patristic Distance matrices
- Transfer Annotations: Fixed crash on circular contigs with annotations extending outside the bounds of a sequence in the alignment
- Translation: When extracting translations from sequences in a list, annotated codon starts are now respected
- Uniprot: Updated search to use HTTPS
- Alternative BLAST: wwwBLAST is no longer supported due to changes in NCBI
- NCBI Popset: Downloading multiple popset documents at the same time resolves to the correct name
- GenBank Export: added an option to replace spaces with underscores in the LOCUS name
- Map reference: Fix crash mapping reads longer than a circular reference sequence when a gap spans the origin halfway through the read
- General: Fix crash starting Geneious using Java 8 in Linux Gnome with font scaling set to less than 0.96
- General: Warn if required lsb package is not installed on Linux
- Licensing: Fix valid FlexNet licenses damaged by OS update or system backup/restore and reported as expired
- Security: Turned off support for External XML Entities
Version 11.0 (5 September 2017)
Patch Versions:
11.0.1
11.0.2
11.0.3
11.0.4
11.0.5
Features:
- Analyze Silent Mutations - Annotate potential restriction sites that can be introduced by silent mutations
- Volcano Plots - Visualize gene expression in an interactive view that synchronizes your selection with the Annotations and Sequence View
- Better Fastq Import:
- Paired reads can now be associated with each other during import and Geneious will do it's best to guess how they're paired
- Read technology can also be set during import (read technology is used by some assemblers)
- CRISPR Improvements:
- Added support for Cpf1 enzyme variant with 5' PAM site
- Added 'Target Sequence' as a qualifier on CRISPR annotations
- Cloning: Create an empty enzyme set via File > New and add enzymes to it
- PCA Plots: Improved label positioning and added a legend
- Sequence/Alignment View: Selections of multiple annotations are now synchronized with the Annotations view
- Sequence/Alignment View: Added annotation filter 'truncated' term which matches annotations with a truncated interval
- Workflows: Added 'Group sequences by name' workflow for grouping sequences with the same name prefix into a list
- CSV/TSV Exporter: Now supports exporting in the compressed .csv.zip and .tsv.zip formats
Fixes and Minor Changes:
- BBTools: Upgraded to version 37.28
- Sequence View: When shift-clicking in circular sequences, the selection is now always made clockwise around the circular instead of selecting the shortest selection
- Sequence View: In wrapped mode, improved performance and fixed transient rendering glitches when scrolling
- Sequence View: Fixed annotating different length sequences with a truncated annotation to keep the truncated status on all sequences
- Sequence/Alignment View: Stopped editing mode getting turned on automatically in some situations where it was unnecessary
- Sequence/Alignment View: 'Create separate annotation for each interval' option now remembers whether it was previously on or not
- Sequence/Alignment View: Fixed crash sometimes when showing annotation results in a separate window
- Sequence/Alignment View: Fixed bug where annotation type occasionally remained off in the controls after an annotation of a new type was added
- Sequence/Alignment View: Fixed a rare crash that can occasionally happen after saving a large document
- Alignment View: Fixed crash sometimes when reverse complementing a circular alignment
- Alignment View: Improved performance when zoomed out while showing translation
- Alignment View: Improved performance when running 'Live Annotate and Predict' on alignments
- Alignment View: Fixed annotations spanning the origin of the consensus sequence not being fully rendered
- Alignment: Fixed incorrect default parameter values for MUSCLE
- Transfer Annotations: Fixed transfer of annotations spanning the origin in circular alignments
- Translation: Added 'Remove final stop codon' option to translation from sequence view
- Translation: Fixed bug turning off 'Remove final stop codon' option would not work on some sequences in workflows
- Backup: Now remembers the last backup location you used, separately from other export operations
- NCBI Search: prevents duplicate download of full documents and fixed possible endless loop when failing to download
- NCBI Search: Fixed crash in some instances when Gene documents don't have a commentary section
- NCBI Search: Added 'Targeted Loci' rRNA databases
- SPAdes de novo assembly: Fixed a fresh install not working on recent versions of Windows
- Import: Fixed crash when importing multiple files when out of disk space
- GenBank Import: Correctly imports all sequences from gb files where some sequences end with a single CONTIG line
- GenBank Export: Fixed crash for some files that don't have an accession
- GenBank Text View: Shows GenBank entries in strict format
- Workflows: Fixed crash when a workflow exposes the alignment automatically determine direction setting and the workflow is then used on protein sequences
- Sequence Extraction: When extracting using the annotations table without concatenating intervals, multi-interval annotations are now truncated (affects interval indices in result)
- Reverse Complement: Fixed crash extracting reverse complement sequence list from medium-size contigs (> 10,000 sequences)
- Start up on Windows: Fixed rare crash on start up
- Shutdown: Fixed hang on shutdown when there is a very large tree document in your database
- Expression Analysis: Added option to calculate expression levels for miRNA, ncRNA, or any annotation type that ends with RNA
- Compare Expression Levels (Geneious method): Fixed weirdly formatted p-values like 0E-39 which should be 0
- Compare Expression Levels (Geneious method) and Calculate Expression Levels: Values produced now have 2dp instead of 1dp accuracy
- Compare Expression Levels (DESeq2 method): Confidence and absolute confidence are now derived from adjusted p-values
- PDF Documents: Fixed crash in some situations after importing a PDF document into Geneious
- Annotate from Database & Test with saved primers: Primer annotations that have identical binding site and extension are now merged
- Primer Annotations: Primers with an extension are now visually different
- Document Table: "Modified" date column is now displayed by default
- Exporting Tables: better default names when exporting Annotation or Restriction Fragment tables
- Tadpole de novo assembly: If Tadpole produces no contigs, all messages produced by Tadpole are now included in message displayed in Geneious
- Map to reference / de novo assembly: Algorithm names displayed in most locations are now shorter. e.g. replaced "Bowtie2 - Fast and accurate read mapper" with "Bowtie2"
- De novo assembly: Added option to specify the minimum number of sequences a contig must contain before it may be circularized (previously this was always 3)
- GFF Import: Fixed crash when importing into a folder containing an alias document
- Preferences: Fixed duplicate entries appearing in the "save selected documents" drop down list
- Performance: Fixed occasional half second pauses in Geneious when showing some dialog windows
- EMBOSS tools: Fix an error when searching for some long motifs
- MacOS installation: Fixed problem running certain bundled plugins when user does not have write access to the install directory
- Chimera Filtering: Update Cygwin DLL bundled with Windows version to 2.8.2 to satisfy security scans even though vulnerability did not affect Geneious
- Geneious Server Database/Shared Database: Fixed a crash that occurs when importing SAM/BAM files and trying to use a reference from the same folder
- Geneious Server Database/Shared Database: Fixed a hang that occurs when losing network during database initialization
- Security: Geneious now uses any CA trusted root certificates installed in the OS for SSL connections
- Security: New Advanced Preferences option SSL.CustomTrustedCertificates allows storing one or more custom trusted CA root certificates for SSL connections
- General: Fix incorrect warning when running under CentOS 7
Plugin Development:
- Exposed option for choosing colors (Options.addColorChooserOption)
- Added method for adding help button next to an option (Option.setHelp)
- Added methods to access selected annotations from annotation generators via SequenceAnnotationGenerator.SelectionRange
- Added method to access the Java binary used by Geneious at runtime (SystemUtilities.getJavaExecutable)
Geneious Server and Geneious Database Server:
- Add support for installation on version 7.x of Red Hat Enterprise Linux (RHEL) and CentOS
- Update to version 7 of Tomcat
- Removed login option to accept untrusted certificates, superseded by SSL certificate related changes in Geneious
- Add support for clusters that do not report status of jobs that have been completed, such as is the default for Univa
Patch 11.0.1 (26 September 2017)
Fixes and Minor Changes:
- Cloning: Optimize Codons operation has move from the Annotate & Predict menu to the Cloning menu
- Plugins: List of installed plugins is now sorted by description by default
- Batch Export: Fixed crash attempting to batch export to a Geneious format version that is not supported by the all of the documents
- BLAST: Fixed crash sometimes when running BLAST on an alias to a deleted document
- Assembly: Fixed bug causing assembly to unselect the document you are viewing while assemble by list is running in the background
- Assembly: Fixed duplicate contig names when assembling by sequence list
- Assembly: Fixed very poor performance in rare situations in the Geneious de novo assembler
- Assembly: When assembling each list separately, if one set produces an error it no longer stops assembly of all other sets from running
- Map to reference: Changed 'only map paired reads which map nearby' to require them to be within insertSize±insertSize*2 and introduced 'which map closely nearby' option for the old behaviour of insertSize±insertSize/2
- Workflows: Added option to record the author of a workflow
- Workflows: Added option to 'Randomly Sample Sequences' workflow to use the first N sequences from the source list (faster than randomly sampling)
- Shared database: Fixed poor startup performance of Geneious sometimes when auto-connecting to a shared database
- Shared database: Fixed crash in change group of folder when user's private group is the only one in which they have sufficient rights
- Shared database: Fixed occasional failure to prevent creation of group with duplicate name, empty string, or with leading or trailing space
- Sequence View: Fixed so that 'save as image' does not scroll to the start of the sequence
- GenBank Importer: Fixed a bug importing flat files where a space was required in DBLINK entries before the accession number (now files with and without the space will import)
- GFF Exporter: Exports sequences in fasta-format at bottom of the file and does not export all-blank sequences
- PCA Plots: Fixed label positioning bug
- Volcano Plots: Fixed crash selecting annotations before viewing plot
- SPAdes: Fixed failure on paired reads that use .1 and .2 instead of the more usual /1 and /2 suffix
- Find CRISPR Sites: Fixed a warning label that was showing up when it did not need to
- Sequence Extraction: Fixed a bug where annotations spanning the origin were split into two intervals when reverse complementing a whole circular sequence, and primers spanning the origin were deleted
- Analyze Silent Mutations: Fixed handling of circular sequences, truncated annotations, and potential restriction sites extending past the final codon
- General: Fix memory leak (and potentially later crash) when deleting a document that is open in a new window
- CM5 Importer: Fixed protein sequence import
Patch 11.0.2 (3 October 2017)
Fixes and Minor Changes:
- CM5 Importer: Now importing notes
- Transfer Annotations: Fixed a bug transferring annotations from circular reference sequences
- Operations Table: Fix spurious duplicate entries for Geneious Server jobs
Patch 11.0.3 (30 October 2017)
Fixes and Minor Changes:
- Analyze Silent Mutations: Fixed crash matching non-palindromic recognition patterns on the reverse sequence
- Workflows: Extract Sequences by Name now separates names by new lines when specifying no separator
- Fastq Import: Fixed crash importing paired reads when one of the paired read files is invalid
- BBMerge: Fixed crash when all reads are able to be merged
- Document Chooser: Fixed bug where it would show some documents from folders that start with the same name even if they're not subfolders
- Translation: When an annotation with a "translation" property has its nucleotides edited this property is renamed to "Original Translation" so that it is not used if the annotation is later translated
- Text View: Fixed bug that would automatically scroll to the end of a text view when it was opened
- De Novo Assembly: Pairwise contigs with a forward and reverse directed read that have not had 'Set Read Direction' used on them, are now consistently orientated so that the read with the first alphabetical name is in the forward direction. Exceptions to this rule can be specified using the advanced preference called 'Assembly.ForwardReverseNamePairs'
- Sequence Extraction: Fixed bug causing annotations with codon_start qualifiers to be wrongly truncated during extraction of multiple annotations
Patch 11.0.4 (13 December 2017)
Fixes and Minor Changes:
- SPAdes: Fixed failing to run when trusted or untrusted contigs have quality information
- De Novo Assembly: Changed default for producing circular contigs to off
- Text View: Fixed occasional bug that would cause infinite pages to be printed when printing text views
- Security: Introduced an advanced preference SSL.useOsKeystore that can be used to turn off using the OS installed CA trusted root certificates
- UI: Fixed some selected buttons not displaying properly on Mac OS X 10.13 High Sierra
Geneious Server and Geneious Database Server:
- Fixed Geneious Server customisation of Tomcat overwritten when CentOS 7 upgrades Tomcat
Plugin Development:
- Fixed bug in example code for creating folder-type plugins in build scripts for most sample plugins bundled with the Dev Kit
Patch 11.0.5 (24 January 2018)
Fixes and Minor Changes:
- BLAST: Prevent crash for sequences that have missing reference documents
- NCBI: Fixed crash when downloading full nucleotide & genome sequences
- UI: Fixed some selected buttons in main toolbar not displaying properly on Mac OS X 10.13 High Sierra
Version 10.2 (9 May 2017)
Patch Versions:
10.2.1
10.2.2
10.2.3
10.2.4
10.2.5
10.2.6
Features:
- Compare Expression Levels: PCA plots for multi-sample RNA-seq data
- Workflows: Added support for cloning operations
Fixes and Minor Changes:
- Workflows: Added buttons to allow reordering of workflow steps
- Workflows: When run on operations that generate annotations on a referenced sequence in an alignment/contig (e.g. Find Variants/SNPs) added an advanced option for whether to propagate the annotations back to the referenced sequence
- Workflows: Replaced 'Truncate Annotations' workflow with 'Modify Annotation Intervals' workflow that also allows extending or shrinking annotation intervals
- Workflows: When an operation in a workflow saves documents to a sub-folder, those documents are now passed on to the next step in the workflow
- Sequence View: On multiple unaligned sequences, the little previous and next buttons for each annotation type now work
- Sequence View: Added "Don't show again" option to the message about there being too many annotation or track types to show them all in the controls
- Annotations Table: Order of columns can now be set under "Manage Columns"
- Document Table: Order of columns can now be set under "Manage Columns"
- Folders: Added "Collapse All" and "Expand All" options to right-click menu on folders that have subfolders
- Folders: Geneious now uses an icon to indicate if a folder is shared with other users, includes folders in a Shared Database or Geneious Server Database
- Shared Database: Folders created under the root folder will now always be created in a user's primary group
- Shared Database: Folders that are not created under the root folder will now always inherit the group of their parent folder
- Shared Database: Fixed a problem that prevented editing of group roles when using Oracle databases
- Shared Database: Fixed a problem that could incorrectly treat a folder as read-only when it was not
- BBTools: Upgraded to version 37.17
- Map to reference: Improved alignment around gaps near ambiguity characters
- Map to reference: Fixed crash using "Assemble each list separately" when one of the lists contains no sequences
- Map to reference: Fixed bug where deletions of repeat regions over 15bp were not being discovered
- Map to reference: Fixed out of memory error when mapping reads (that should fail to map due to exceeding the maximum number of mismatches allowed) spanning the origin of a circular reference sequence
- Assembly / Map to reference: output contigs and consensus sequences record the algorithm used in the document description
- SPAdes assembler: Fixed so that if you are using an unsupported version of Windows, you can still run SPAdes on Geneious Server
- SPAdes assembler: The trusted and untrusted contigs options no longer default to the same trusted/untrusted contigs as you used for the previous assembly
- Contig View: Added option to sort reads by the number of differences from the reference sequence on contigs with fewer than 10,000 reads
- Sequence Extraction: Fixed crash extracting a region while also viewing an empty sequence
- Sequence Extraction and Merging Paired Reads: The 'Read Technology' field (and other fields) are copied to the derived documents
- Sequence Extraction and Translation: Fixed bug where translations were wrong after extracting a partial annotation on a circular sequence
- Copy Translation: Fixed crash copying from a circular sequence when the first codon spans the origin
- Alignment: Fixed crash sometimes when aligning after reverse complementing a sequence containing a mixture of DNA and RNA
- Alignment: Fixed crash when running MUSCLE on Windows when running from a data directory containing certain non-Latin characters (e.g., Chinese)
- Alignment: Fixed crash when running MAFFT on sequences containing inosine with "Automatically determine sequences' direction" turned on
- Gibson Assembly: If sequences are compatible it doesn't create primers and doesn't warn about filled in overhangs
- Gibson Assembly: RNA sequences used to create an invalid warning in the report about the reverse primer binding at multiple locations
- Cloning: Fixed crash when existing overhang annotations were adjacent to a cut site or PCR
- Cloning: Display warnings if similarity of overhangs is above threshold
- Gateway Cloning now records the used intervals and shows them in the lineage
- Lineage: Fixed incorrect interval when extracting a region across the origin from a circular sequence while viewing multiple sequences
- Primer Annotations: Fixed crash when trying to create a primer from an annotation that is between two bases
- Compare Expression Levels: Fixed crash that would occur when DESeq2 received a count table containing at lease one zero per gene
- Compare expression levels: Fixed crash when using Geneious method on multiple reference sequences when the first reference sequence does not contain both tracks
- SAM/BAM Export: Improved performance on data with high coverage paired reads (2 to 3 times faster)
- Tree Building: Fixed crash that could occur when building trees out of alignments backed by GenBank documents in some tree builders
- Tree Building: Fixed crash that could occur when cancelling a tree building operation on unaligned sequences
- Tree View: Fixed missing attributes from "Show branch labels"
- 3D Structure View: Fixed background CPU usage sometimes after closing a view that was using the 'Spin' effect
- Data Location: Fixed crash after moving your Geneious data to a location that Geneious is unable to properly access (e.g. due to free low disk space)
- Repeat Finder: Fixed crash when finding repeats in the selected region only when the selected region spans the origin of a circular sequence
- Apply Variants to Reference Sequence: Fixed crash when running it on a sequence without variant tracks
- Find Variations/SNPs: Fixed incorrect protein effect for some start codon variants that would translate as M in a start codon but would translate differently at other positions (e.g. CTG translates as M as a start codon, but L elsewhere)
- Find Variations/SNPs: 'Protein Effect' field now says 'Start Codon Loss' if the start codon translation changes from M to a different amino acid
- Wrapper Plugins (e.g. RAxML, FastTree, Garli): When saving terminal output that is too long, the text will be truncated such that the first and last 500 lines are always retained
- Newick Tree Export: Fixed bug where exporting MrBayes trees with support values failed to save support values
- Document Notes: When text is too long to display in the "Info" tab, the text will be truncated such that the last 1000 characters are still shown
- Printing: Fixed hang that could happen when printing documents as images or PDFs
- General: Fixed crash sometimes when double clicking menu items
- General: Gracefully fail instead of crashing when Geneious data is in a Jottacloud synced folder which creates conflicting synchronization files
Geneious Server:
The Geneious Server Database has undergone a number of changes that make it more suitable for deployment in an enterprise environment.
- Automatic creation of a private folder group for each user
- New database administrator settings. These are enabled for new databases, disabled for existing ones and can be changed at any time:
- Assign new folders under the root folder to the user's private group instead of the user's primary group
- Allow regular i.e. non-admin users to create and change the group of folders themselves
- Prevent users from storing new documents in the root folder
- "Show Inaccessible Folders" option is no longer available for Geneious Server Database
- Logging of events that affect user access to documents
Patch 10.2.1 (30 May 2017)
Fixes and Minor Changes:
- Tree Building: Fixed crash with third-party tree builders that don't provide any user-defined options
- BLAST from workflows: Fixed bug where it would use the default database instead of the selected database when run on a nucleotide sequence list
- Alignment Extraction: Fixed out-of-frame inline translation on alignments extracted from alignments when the extraction starts with an internal gap
- Workflows: Fixed bug where adding a new step would sometimes add it to the end of the workflow instead of after the currently selected step
- Sequence Editing: When deleting nucleotides from the start of a CDS annotation, the codon_start property is automatically adjusted to keep the translation of the remaining section of the annotation the same as it was previously
- Alignment/Contig View: Annotation tooltip 'Length' field has been renamed to 'Length (with gaps)' and a new 'Length' field introduced which contains the ungapped length
- Save as Image: Fixed sequence numbering getting slightly clipped sometimes on the right hand side of the image
- Restriction Cloning: Fixed bug where Workflows always used Enzyme Set instead of Annotated Enzymes, or where it couldn't be selected if the initial document didn't have annotated enzymes
- Restriction Cloning: Fixed poor performance when digesting large sequences into fragments
- Document Searching: Track names and properties on newly created or edited sequences are now indexed for searching in local and shared databases
- Document Searching: Improved speed for searches on large shared database
- Nexus Tree Importer: Internal node attributes can now be specified as branch support values or node labels and will behave appropriately when rerooting
- CSV Exporter: Better handling of descriptions that contain elements that look similar to html < tags /> but aren't
- De novo assembly: Fixed crash when using Windows 10 Insider Preview
- De novo assembly: Fixed crash in rare situations when the 'circularize contigs' and 'produce scaffolds' settings are both on (they are both on by default)
- Start up: Fixed crash on startup in rare situations on Windows
- NCBI Search: Fixed cases where summary documents were shown multiple times if connection was interrupted while the search was running
- Find Variants/SNPs: Fixed crash when setting strand-bias threshold to 50% when reads contain ambiguities
- NCBI Download: Fixed bug where genome summaries were not replaced by the full downloaded document if the summaries don't have a version number
- Printing/Saving As Image: Fixed bug where saving an image of an entire circular sequence while zoomed in would omit annotations outside the viewed region
- Find Heterozygotes: Fixed bug where no heterozygotes were found if only the left-hand end of the sequence was annotated as trimmed
- GenBank Document Exporter: When exporting strict GenBank format, annotation names are now saved as 'standard_name' qualifiers
- BBTools: Upgraded to version 37.25
- Sequence Extraction: When extracting a primer or probe from a sequence list the resulting document is now of type Oligonucleotide
- Optimize Codon Usage: Fixed bug running from Workflows where result sequence was identical to input
- Geneious Server Database: Fixed a bug where connection errors on startup would cause the database to be removed from Geneious
Plugin Development:
Geneious Server:
- Fixed a bug where the new database administrator settings introduced in 10.2 were not initialized correctly and displayed the wrong values for new databases
- Fixed a bug where multiple dialogs would be displayed when user was disconnected
- Fixed various other bugs related to new settings introduced in 10.2
Patch 10.2.2 (6 June 2017)
Fixes and Minor Changes:
- Save as SVG Image: Added option to draw text as images so that the saved image more accurately matches what Geneious displays
- Save as PDF Image: Saved PDFs now use the same font as displayed in Geneious
Patch 10.2.3 (11 July 2017)
Fixes and Minor Changes:
- Optimize Codons: Restriction site annotations will now be recalculated instead of being copied across, which could previously introduce errors
- Geneious Server Database/Shared Database: Stop showing a message dialog each time the server is disconnected
- Geneious Server Database/Shared Database: When changing the group of a folder, the apply to subfolders option is now off by default
- Geneious Server Database/Shared Database: Admin group role now required to change folder groups (except with Geneious Server Database connection and setting for "All users" can manage groups)
- Geneious Server Database/Shared Database: Fix error when adding new user with primary group of User Private with external authentication
- Geneious Server Database/Shared Database: Remove restriction that a folder can have Private group only if all folders in its tree do
- Geneious Server Database/Shared Database: Make browsing folder in large database much faster than 10.1
- Geneious Server Database/Shared Database: Fix problem that caused 'doesn't contains' searches to return the wrong results
- Geneious Server: Fix Univec BLAST database used for trimming
- Icons: Shared folders will now have an icon overlay the same colour as their default colour on every distribution
- Generate or Extract Consensus Sequence: The Ambiguities field is no longer copied to the full or partial consensus sequence since it could be incorrect if only a partial sequence is extracted. This field is still automatically calculated on full or partial sequence extractions with quality information
- FastQ Export: Spaces in sequence names are no longer replaced with underscores by default; this can be changed by setting an advanced preference
- Copy Translation: Fixed crash copying translation from selected truncated annotation
- SAM/BAM Import: Fixed crash in rare situations when important SAM/BAM files
- General: Fixed bug where operations sometimes deleted all annotations from source document
- UniVec: Updated the bundled UniVec database to the latest version
- Import: GenBank Flat format importer now recognizes file with .seq extension
- Import: Sets correct dates for VectorNTI files that previously showed dates before 1995
- Import: Multi-Interval annotations in GenBank files exported by VectorNTI are imported to the correct location
- Import/Export/Backup: Fixed Geneious suddenly exiting during import/export under Windows 10 Creators Update when GodMode is enabled
- NCBI Blast: Fixed crash when running blastx with a query that has editing annotations that need to be reverted
- General: Fixed crash in some situations when out of disk space
Patch 10.2.4 (14 February 2018)
Fixes and Minor Changes:
- NCBI: Fixed crash when downloading full nucleotide & genome sequences
- NCBI: Warn if NCBI fails to return all the expected accessions
- Shared Database: Fixed a crash that occurs when importing SAM/BAM files and trying to use a reference from the same folder
- Shared Database: Fixed crash in change group of folder when user's private group is the only one in which they have sufficient rights
- Alignment View: Fixed crash or incorrect sequence data after sorting an alignment with a reference sequence, editing some sequences, and then saving
- General: Fix incorrect warning when running under CentOS 7
Patch 10.2.5 (1 May 2018)
Fixes and Minor Changes:
- NCBI Sequence Search: Fixed crash when a document doesn't specify a molecule type
- NCBI Sequence Search: Fixed rare crash when contigs don't have a 'join()' statement
- BLAST Query centric alignments: Multiple hits matching repeated regions are now distributed correctly across those repeats
- Licensing: Upgrade FlexNet executables on Linux for compatibility with Ubuntu 18.04
Patch 10.2.6 (17 July 2018)
Fixes and Minor Changes:
- Uniprot: Updated search to use HTTPS
- Licensing: Fix valid FlexNet licenses damaged by OS update or system backup/restore and reported as expired
- Security: Turned off support for External XML Entities
Version 10.1 (7 February 2017)
Patch Versions:
10.1.1
10.1.2
10.1.3
Features:
- RNA seq expression analysis: Compare Expression Levels now has option to use DESeq2 for pairwise analysis with replicate samples
- Annotate from Database: Will annotate nucleotide sequences from a protein database by comparing translations of the nucleotide sequence in all six frames with the protein database sequences
- Gibson Assembly: Can now save the primers used
- Gibson and Golden Gate: Now has sequence view of fragments within the options
- Import: Zip files containing multiple files and sub-folders can now be imported
- Sequence View: Added 'Copy Translation' to translate selected regions of a nucleotide sequence (in right-click menu)
- SPAdes de novo assembler: For MacOS/Linux: 64 bit OS is required. For Windows, 64 bit Windows 10 (with recent updates installed) is required. You also need to install additional Windows features (Instructions)
- Find CRISPR Sites:
- Major performance improvements were made to the off-target scoring algorithm
- Speed and Filter strategies were removed because off-target scoring is no longer a rate-limiting step. This means all CRISPR sites will now be scored against all potential off-target sites in every run
- Scoring CRISPR sites against off-targets now takes a seed region into account. This is a 10 bp region adjacent to the PAM site that can tolerate a maximum of 2 mismatches and 0 indels
Fixes and Minor Changes:
- Folder Navigation: When selecting additional folders, the selected documents in the original folder will now remain selected
- Find Motif: Fixed hang showing options on large contigs
- NCBI BLAST: Detects Inosines in queries before submission and fails more gracefully
- NCBI BLAST: No longer crashes when trying to write Blast results to a read-only folder in a shared database while Geneious is shutting down
- NCBI BLAST: Added an option to set Max Target Seqs to make this setting independent from the Maximum Hits option
- NCBI BLAST: Sort database options alphabetically, set nr as default & slightly adjust their names
- De novo assembly: Fixed crash sometimes when insufficient memory is available
- De novo assembly / Map to reference: When saving in a sub-folder when assembling by name or list, the document names now uses the specified name template in addition to the folder name using the name template
- Map to reference: When mapping to multiple reference sequences from the same list the assembly name no longer appends "x sequences" to the reference sequence name within the document or folder names
- Map to reference: Fixed poor performance when using thousands of reference sequences when nothing maps to most of those references
- Map to reference: If you use a reference sequence from the selected documents that is not the one Geneious guesses you want, then if you run with the same reference sequence again, it now defaults to your preferred reference sequence
- Map to reference: Fixed map to all locations sometimes excluding locations on the other strand when the alignment could contain different but equally valid positions for gaps
- Map to reference: The 'Trim paired read overhangs' setting is now applied before choosing the best mapping location so that reads don't incorrectly map to a location that more closely resembles the untrimmed adapter sequence
- Map to reference: Fixed to not ignore trim annotations that overhang the ends of the read
- Map to reference: Fixed crash when reference sequence is modified while mapping is in progress
- Map to reference / de novo assembly: Improved results on data with gappy error models (e.g. Ion Torrent, PacBio)
- Map to reference / de novo assembly: Fixed bug where the 'Sample Name' field value on the results would be lost after restarting Geneious
- Compare Expression Levels: You can now select all contigs from multiple samples at once and the documents will automatically be grouped together by sample when calculating expression levels
- Alignment View: Fixed hang/very poor performance viewing large alignments built from multiple sequence lists
- Contig/Alignment View: Fixed crash sometimes when viewing large contigs or alignments
- Contig/Alignment View: Fixed so that editing by dragging bases or gaps in the reference sequence works
- Contig/Alignment View: Improved performance when replacing all characters in a single column
- Contig/Alignment View: Fixed rare crash when extracting consensus sequence from very large contigs
- Contig/Alignment View: Fixed incorrect statistics when selecting reads spanning the origin of circular contigs
- Contig/Alignment View: Fixed crash while viewing the sequence logo graph and deleting sequences from a large contig
- Sequence/Alignment View: Fixed annotation resize boxes for the selected annotation not being drawn on the first sequence
- Sequence/Alignment View: Improved performance viewing 10,000+ annotated sequences
- Sequence View: Fixed rare hang
- Sequence View: Fixed situation where some annotation qualifiers were not offered as labels for that annotation
- Sequence View: Reduced memory usage viewing 100,000 or more annotated sequences
- Sequence View: Fixed rare crash when viewing empty sequences with the mini-map visible
- Sequence View: When zoomed out, annotations that only slightly overlap are drawn adjacent to each other instead of being drawn in separate rows
- Annotate from Database: Runs faster by using multiple processors
- Transfer Annotations: When the ends of an annotation corresponds with gaps on the target sequence, extends the annotation on the target sequence to include that many extra non-gaps
- Apply Variants: Fixed incorrect results from diploid homozygous variants imported from VCF format
- Tree View: Branch display now defaults to branch support if last used value is not found
- Tree View: "Show next to node" option added to branch display options
- Tree View/Newick Tree Importer: Internal node labels can now be specified as branch support values or node labels and will behave appropriately when rerooting
- Newick Tree Importer: Fixed bug where user-specified label was ignored for explicit branch labels
- Trim Ends: When trimming stand-alone sequence documents, fixed so that it doesn't add two document history entries. This also improves performance
- Trim using BBDuk: The description on the untrimmed sequences is now copied onto the trimmed sequences. The BBDuk summary information previously included in the description is available in the info tab
- Translation: Fixed bug where annotations on the edge of the translated region were wrongly included in the translated sequence
- Consensus Calling: Added 65% threshold option
- Extract Annotations: Added option to only match annotations that are not truncated
- Extract Annotations: Fixed occasional crash when annotations without intervals are present
- Created Date: Fixed various situations where the created date of new documents took on the created date of the document it was derived from
- Workflows: Can now copy and paste workflow steps and ctrl-drag duplicates a workflow step
- Workflows: Translation step now allows translation in frames other than frame 1. Also added options to turn off using alternative first codon table and keep trailing stop codons
- Workflows: If a custom code workflow crashes due to a bug, the Geneious error message now includes the line number and the line of code causing the crash
- Workflows and Batch Export: Fixed to no longer load all the documents into memory prior to running
- Operation Profiles: Fixed operation profiles not being available when running some operations on multiple documents
- Operation Profiles: Fixed crash when using operation profiles with some 'Annotate & Predict' operations on multiple sequences
- Lineage View: Fixed the 'Go to' button sometimes not selecting the correct region in the target sequence
- Geneious Aligner: Fixed aligner not properly handling cancellation on larger datasets
- Shared Database: Fixed a bug where "Document type is not" searches would often still contain documents of that type
- Shared Database: Fixed rare failure when connecting over a slow network connection
- Shared Database: Correctly disable right click menu editing actions for read-only folders
- Fragment View: Fixed crash when looking at 0-length sequences
- Cloning: Shows different recently used backbones for Gibson Assembly, Golden Gate & Restriction Cloning
- Cloning: Shows warning if pre-digested overhangs have different length to provided enzymes & fails to introduced new cut sites for that overhang via PCR
- Cloning: Detail view only highlights the part of the sequence that will be in the result, without highlighting primer extensions that aren't on the sequence yet
- Cloning: Clear the detail view when vectors or inserts get removed
- Golden Gate: Fixed crash when performing a PCR using a primer with extension shorter than the overhang sequence of the selected enzyme
- Golden Gate: Fixed crash when using annotated primers for GenBank-derived documents
- Golden Gate: Fixed displayed sequence range and length in construct layout when using annotated primers
- Restriction Cloning: Fixed a bug where it wrongly showed internal cut sites as external if a circular sequence used the same cutsite for both reactions
- Find CRISPR Sites: Fixed bug that in some cases was silently filtering out offsites with ambiguities in the PAM region that should be considered
- Find CRISPR Sites: Fixed bug where some offsites were counted twice in off-target scoring in some situations
- Calculate Expression Levels: Meta Data (notes) from the mapped contig is now copied to the track properties of the expression level track
- Group Sequences: Fixed grouped sequences using and old version of their description sometimes
- Download Full Documents: Fixed bug where if you start a download then view a document in another folder while the download completes, running an operation treats the downloaded document as being wrongly selected
- Deleting Folders: When deleting multiple selected folders, no longer shows a confirmation dialog for each folder
- Deleting Folders: Fixed crash when deleting hundreds of folders at once
- Import: Fixed crash sometimes when importing multiple separate files and grouping those sequences into a list
- Import: Artemis importer is now disabled to avoid confusion. It can be turned back on via Customize Feature Set in the Plugins and Features preferences
- VCF Import: Fixed crash when vcf file contains an invalid FORMAT or INFO type
- VCF Import: Add support for Character type in INFO and FORMAT
- GenBank Import: fixed issues where authors were separated wrongly by comma, date was updated on import & better comment formatting
- Plugin Installation: Fixed occasional crash when uninstalling or upgrading a plugin
- Restore Backup: Fixed crash on Windows when restoring a backup on to a network drive
- Start-up: Improved performance so that Geneious starts about 20% faster now
- Start-up: Now retries if the _JAVA_OPTIONS environment was present and Geneious failed to start
- Shutdown: Fixed hang on shutdown
- Protein Statistics: No longer crashes when encountering an unknown state in a nucleotide sequence
- Annotations Table: Fix occasional crash when sorting annotations
- Data location: When moving data to a new location on Windows fixed bug causing duplicates of some files to be left in the old location
- Data Location: Fixed crash if you externally move your Geneious data location while Geneious is running
- General: Now setting the default maximum memory on Mac OS based on total system memory
- General: Fixed hang when running low on memory
- General: Fixed crash sometimes when deleting lots of documents or folders
- General: Fixed poor performance in some cases after heavy use of Geneious, even after restarting Geneious
- General: Fixed poor performance after having worked with 10,000+ annotations that all have unique property names, even after restarting Geneious
- General: Fixed memory used by a large document not getting freed until a new document is loaded
- Licensing: Added option to activate by logging in to a Geneious Account
Geneious Server:
- Fixed poor performance logging into Geneious Server when you have previously run lots of operations
Patch 10.1.1 (27 February 2017)
Fixes and Minor Changes:
- NCBI: Uses Accession.Version numbers rather than GIs (GI numbers are being phased out by NCBI)
- Map to reference / de novo assembly: Properties (i.e. values added in the Info View) of the reads are now copied to all contigs produced (previously these were only copied to small contigs)
- Map to reference / de novo assembly: Fixed some consensus options (e.g. trim to reference sequence, call N if low coverage) not being applied when the reads being assembled have no quality
- Map to reference / de novo assembly: On machines with at least 16 processors, assembly uses one processor fewer in order to leave a processor for garbage collection to prevent runaway memory usage on powerful machines. This can be configured with the advanced preference called MaximumThreads.ReduceByWhenAtLeast16Processors
- DESeq2 Compare Expression Levels: Fixed incorrect handling of replicates, added support for multiple chromosomes, improved documentation, improved performance, fixed coloring of results
- BBTools: Upgraded to version 36.92
- Translation: Extracting a translation to a new document from a CDS annotation now respects the NCBI annotated translation property (which should include the effects of NCBI transl_except properties)
- Transfer Annotations: Added option to not merge annotations of the same type and region into a single annotation
- Transfer Annotations: Prevented transfer of annotations that are completely or partly outside of the reference sequence and can't be truncated
- Annotate from database: Now works with BLAST results in the source database
- Find Variants/SNPs: On circular contigs without a reference sequence, removed incorrect additional variants found past the wrap around position
- Workflows: Added advanced option in workflow steps called 'If this workflow step fails, silently continue using only successful data sets'
- Workflows: Added 'Extract Reads from Contig/Alignment to List' to operations which can be added as a workflow step
- Workflows: Improved 'Group Sequences into List' step to produce more efficient lists when grouping stand-alone sequences
- Workflows: Fixed bug where they would produce inconsistent results on operations that used enzyme set options (because they would use the most recently selected enzyme set from a non-workflows operation)
- General: Fix bug where many operations would unnecessarily load the entire document before showing options
- General: Fix bug where right clicking in folder tree doesn't select the clicked-on folder
- General: Fix bug where 'between base annotations' of GenBank files are not handled correctly
- General: Added advanced option in Preferences to set user name to be used when recording document history
- General: Fixed crash on systems that don't support custom cursors
- Sequence View: Now records the user name of the person responsible when an annotation is created or edited (uses the same name as document history)
- Sequence View: Text inside annotations in the circular view is positioned a bit further away from the edge of the annotation if possible
- Sequence View: Fixed crash in rare situation when deleting primers
- Sequence View: Fixed crash editing in the circular overview while an operation is running on that sequence
- Sequence View: Fixed crash when saving a sequence with large tracks while an operation is running on that sequence
- Set Paired Reads: Added option (default on) to delete the unpaired source documents when pairing by pairs of sequence lists
- BLAST: Updated Geneious default values to reflect default values on NCBI BLAST website
- NCBI BLAST: Display more information about some NCBI Server failures
- Custom BLAST: Fix bug where creating a BLAST database from BLAST hits causes full download to fetch from original BLAST database
- Custom BLAST: Update executable files for 32-bit platforms to their respective latest valid release
- Cloning: Ligate and Concatenate sequences with compatible overhangs no longer discard annotations located within reverse-directed overhangs
- Lineage: Information about extracted annotations and regions are now updated for active links when parent sequence gets modified
- Online Resources: Quickstart Guide link has been replaced with a link to our Quickstart video
- GenBank Files: Fix crash when parsing Comments section where automated annotations don't have an end-tag
- Document Table: No longer displays columns if none of the documents have a value for that column
- Convert to Oligo: When reconverting an existing oligo, will now respect the binding region rather that recalculating for the entire oligo
- Convert to Oligo: Will now always replace any standalone sequences in the selection. Previously, would only replace them if every document in the selection was a standalone sequence
- Geneious Server: Fixed crash in some situations when downloading results from Geneious Server to a different computer than that which ran the operation
Patch 10.1.2 (7 March 2017)
Fixes and Minor Changes:
- NCBI: Fixed a problem where agents would re-download entries that had already been retrieved in the past
Patch 10.1.3 (21 March 2017)
Fixes and Minor Changes:
- Fix crash when changing displays in Linux
- Sequence/Alignment View: Fixed pressing enter in filter text not jumping to correct annotations if enter was pressed earlier while filtering was still in progress
- Sequence/Alignment View: Don't show track tooltip when over the track drop down menu
- Sequence/Alignment View: Fixed crash when saving after adding annotations to the consensus sequence of a blastx result
- Trim Ends on alignments: Fixed hang when choosing the option to remove trimmed regions (instead of annotating them)
- De Novo Assembly: Fixed crash on some non-English language versions of Windows
- De Novo Assembly: The limit for the maximum contigs saved can now be set as low as 1 (previously 100 was as low as it could be set)
- Map to reference: Fixed crash (or minor mis-alignment of reads around insertions) sometimes when structural variant discovery is on
- Golden Gate: Fixed incorrect lineage interval for circular documents when no PCR required and selected region crosses the origin
- Gibson Assembly: Better handling of already compatible overhangs and Gibson Primer Extension annotations
- Restriction Cloning: The ends of linear constructs can now be digested back to any selectable restriction site
- Restriction Cloning: Fixed crash for when propagating changes if enzymes could cut directly next to each other
- Find Restriction Sites: 'Must cut between' now finds enzymes that cut outside their recognition sequence if the region was limited to exactly the cut region
- Printing: Fixed an issue where lines were occasionally skipped when printing text views, including Assembly Reports
- Tree View: External nodes are now correctly highlighted when hovering over their labels in zoomed in views
- DESeq2: Fixed libraries installed by another program being used by Geneious on Windows and Mac
- CRISPR: Put the PAM sequence in the annotation so that it can be filtered on
- CRISPR: Got around crash that could happen when discovering CRISPR sites with high levels of ambiguity
- Primers: Fixed incorrect GC content and other Document Table fields on primers extracted from a sequence list using Convert to Oligo
- Primers: Made it so that GC content is calculated by Geneious (not Primer3) and as such is always present
- Workflows / Licensing: Fixed crash sometimes after viewing workflows and then deactivating your license
- RNA seq expression analysis: Fixed a bug where tracks with no condition were being considered a third condition
- NCBI: Full accession which includes the version is now included in the Accesion field
- NCBI: Fixed a bug that could cause the download of an out of date version of a sequence when using an old summary document. Now downloads the most recent version
- General: Fixed a rare crash that could occur on startup
Version 10.0 (30 August 2016)
Patch Versions:
10.0.1
10.0.2
10.0.3
10.0.4
10.0.5
10.0.6
10.0.7
10.0.8
10.0.9
Features:
- Restriction Cloning:
- Completely redesigned to be much simpler and more powerful
- Automatic identification of compatible cut sites from any number of annotated or un-annotated enzymes
- Manual controls for choice of cut site and treatment of sticky ends such as blunting and filling
- Digest and ligate any number of sequences in one step with drag and drop ordering of fragments
- Embedded sequence view shows target region for each fragment
- Alignment Masking:
- Mask alignment sites that should be excluded when tree building by adding a Masked annotation to the consensus instead of deleting the site completely
- Choose whether or not to exclude masked sites when running any of the tree builders available for Geneious
- Choose whether to gray-out or completely hide masked sites in the Alignment View
- Automatically mask sites according to various criteria using 'Mask Alignment' in the Tools menu (previously called 'Strip Alignment Columns')
- Store multiple alternative masking patterns on the same multiple alignment using annotation tracks
- Import masks from the EXSETs defined in the ASSUMPTIONS block of NEXUS files
- New option to mask or strip sites according to user-defined ranges of sites, or strings of 0's and 1's using 'Mask Alignment' in the Tools menu
- Mask Alignment now ignores trimmed regions of sequences when determining if a site contains ambiguous states
- Mask Alignment now ignores end gaps when computing the percentage of gaps (for contig alignments only)
- Mask Alignment now ignores gaps when determining if a site contains all identical nucleotides/amino acids
- Chimera Filtering:
- Filter chimeric reads from sequencing data by comparing to a reference database using 'Remove Chimeric Reads' in the Sequence menu
- Choose between the bundled public domain UCHIME algorithm or the faster USEARCH implementation (USEARCH must be downloaded separately)
- Use any sequence list or alignment as the reference database, links and instructions for importing suggested databases are included
- Parent/Descendant Improvements:
- Lineage View is now easier to access as a separate tab
- View the options used when an operation was run by clicking 'Show Options' in the Lineage View (for supported cloning operations only)
- Even more information about operations is now shown in the Lineage View
- The region of sequences used in an operation is now shown next to each sequence in the Lineage View
- 'Go to' in the Lineage View now selects the region of a sequence that was used
- Assembly:
- Structural Variant Mapping: Adding support for insertion discovery when the ends of a read map to nearby locations but the center of the read doesn't map
- De Novo Assembly: Better results when assembling Ion Torrent, 454, and PacBio CCS data
- Map to Reference: Better results when mapping Ion Torrent, 454, PacBio CCS and PacBio CLR data
- Map to Reference and De Novo Assembly: Faster on long reads (e.g. PacBio)
- Sequence/Alignment/Contig View:
- Circular Overview: Added a setting to show a zoomed out overview of circular sequences
- Total number of non-gap nucleotides or amino acids now shown in Statistics tab
- Three letter amino acid codes can now be shown by zooming in to 200% on protein sequences or by turning on 'Three letter amino acids' in the translation controls for nucleotide sequences
- Sequences that contain a selection or have the cursor in them are highlighted with a different background color
- Go To Base now allows selection of region that crosses the origin for circular sequences
- Shortcut key added for editing the selected sequence's name or other displayed field (default F2)
- Scroll past the origin of circular sequences using scroll wheel, panning or left/right arrow keys
- Clone Manager Import for molecule files (.cm5)
- Text Document creation and editing - Create a blank text document via File > New and edit plain text documents inside Geneious
- Variant Finding / SNP Trees: Added a workflow to apply discovered variants to the reference sequence in order to create a variant sequence. This is useful for the creation of SNP trees
- New Sequence: Added the ability to specify a binding region to simplify entering primers or probes that have extensions
- Cloning: Create active parent/descendant links when pasting a sequence using 'Paste with Active Link' in the right-click menu of the Sequence View
- Aliases: Store a single document in multiple folders simultaneously using 'Paste Alias' in the Edit menu or by holding Ctrl+Shift when dragging (Cmd+Alt on macOS)
- Folder Search: Find folders by name in the Sources Panel by typing a keyword and pressing Enter
Fixes and Minor Changes:
- Sequence/Alignment/Contig View: When showing numbering on all sequences, fixed so that reversed reads are always numbered in reverse
- Sequence/Alignment/Contig View: Fixed small rendering glitches for single bp annotations in some situations
- Sequence/Alignment/Contig View: Fixed poor performance / out of memory when deleting millions of sequences
- Sequence/Alignment/Contig View: Add annotation no longer creates additional intervals for regions between nucleotides in some situations
- Sequence/Alignment/Contig View: Fixed crash when trying to apply trimming results to an unselected document after starting another operation on it
- Sequence/Alignment/Contig View: Fixed crash in some situations when undoing while live annotate & predict annotations are showing
- Sequence/Alignment/Contig View: Fixed poor performance (and occasional crash) when running low on memory while loading a large annotation track
- Sequence/Alignment/Contig View: Fixed rendering bug on Linux platforms where parts of reference sequence and consensus are drawn over the top of reads in rare situations
- Sequence/Alignment/Contig View: Fixed hang or poor performance sometimes when alt/command dragging a region to zoom to
- Sequence/Alignment/Contig View: Fixed when extracting regions containing duplicate annotations (e.g. FreeBayes variant calls with ploidy 2) to preserve duplicates rather than converting to a single annotation with duplicate intervals
- Sequence/Alignment/Contig View: Fixed incorrect highlighting of differences in reads spanning the origin of circular contigs when hiding columns of gaps
- Sequence/Alignment/Contig View: Fixed integer overflow when drawing annotations on very large circular contigs and sequences
- Sequence/Alignment/Contig View: Fixed crash sometimes when saving after deleting sequences
- Sequence/Alignment/Contig View: Added advanced setting to control the threshold for the number of sequences above which editing history annotations aren't created
- Sequence/Alignment/Contig View: When extracting an unapplied 'Live Annotate & Predict' annotation, that annotation is now included in the extracted sequence. This also fixes a crash when extracting an unapplied primer annotation
- Alignment/Contig View: Fixed poor performance viewing large contigs with coloring by annotation on or wrapping on
- Alignment/Contig View: Fixed consensus name missing when wrapping is on
- Alignment/Contig View: Improved performance when viewing large contigs and increased threshold to allow viewing more reads before it hides reads when zoomed out too far
- Alignment/Contig View: Fixed unnecessary prompt about applying changes to referenced sequences after transferring annotations to the consensus sequence.
- Alignment/Contig View: Fixed crash after extracting sequences when the same alignment has unsaved changes in another window
- Alignment/Contig View: Removed incorrect warning about editing when pressing a shortcut key containing ctrl and shift on MacOS
- Alignment/Contig View: Fixed crash sometimes when running tools which annotate sequences
- Alignment/Contig View: Fixed consensus annotations discarded when extracting an alignment from an alignment
- Alignment/Contig View: Fixed the names of tracks with long names being rendered over the top of annotations on alignments that also contain a tree
- Sequence View: Fixed number of bp selected message appearing in wrong location sometimes while dragging on a circular sequence
- Sequence View: Fixed 'Go to base' crash when choosing to select a different sequence from a genome sequence list
- Sequence View: Fixed crash when switching between large annotated linear and circular sequences in the sequence selector
- Alignment/Tree View: Fixed edit of field in Alignment View not propagating to corresponding tip label in Tree View
- FASTQ and FASTA paired read exporters: Improved performance and also now works on contigs
- Coverage Graph: Fixed to not draw log scale label when there isn't enough space for it
- Sequence Logo Graph: Fixed crash on large contigs after flagging the reference sequence as not a reference sequence
- Wrapper Plugins: Fixed crash when running a newly created wrapper plugin on a non-matching set of selected documents
- Tree Building: Fixed crash if you delete sequences from a list so that there are under three sequences, then run tree building and save changes when prompted
- Tree Building: Changed Jukes-Cantor equation used to calculate protein sequence distance matrix to be more accurate
- Translation: Fixed poor performance working with translations of millions of sequences
- Annotations Table: Fixed Geneious becoming unresponsive while exporting a large table to CSV
- Document Table: Fixed Paste Reverse Complement and Paste Without Annotations for multiple documents, Sequence Lists, and Alignments
- Map to reference: Fixed crash when a paired read in an existing contig was flagged as the reference sequence
- Map to reference: Fixed map to all locations sometimes excluding locations on the other strand when the alignment could contain different but equally valid positions for gaps
- Map to reference: Fixed excessive memory usage when mapping large contigs to a reference sequence
- Map to reference: Fixed excessive memory usage and poor performance when iteratively mapping to a very large reference sequence
- Map to reference: Fixed mapping reads to all locations sometimes not mapping gappy reads to all inverted repeat regions
- Mask Alignment: Sequences containing only gaps are excluded from the result when stripping sites
- Mask Alignment: Fixed wrongly removing annotations present on the consensus sequence
- Assembly Options: If trim options inside assembly options have been modified from default values, the trim "Options" button now indicates that by changing its label
- BBTools: Upgraded to version 36.11
- Trim using BBDuk: Added link to actual sequences used for bundled adapter lists
- Trim using BBDuk: Turned on 'Keep original order' setting by default to ensure that rerunning it produces the same results each time
- Error Correct and Normalize Reads: Exposed number of threads setting since results vary depending on the value of this setting
- NCBI: Added option to search and download non-refseq sequences from the Genome database
- BLAST: Fixed crash if you delete the the folder containing the results while BLAST is running
- BLAST: Fixed BLAST giving incorrect results when running a Discontiguous Megablast due to parameters being incorrect
- BLAST: Fixed a problem where NCBI BLAST always used the default match scoring values regardless of what was chosen
- BLAST: Fixed BLAST not importing all result from search or file
- BLAST: Updated BLAST+ executables to v2.4.0
- Custom BLAST: Fix a problem where downloading/setup process of custom BLAST does not recover from network failure
- Custom BLAST: When a large batch blast is cancelled we now immediately stop all iterations of that job
- Document History: When viewing options that have other options accessible via a button (e.g. the trim options inside assembly options), the button is now enabled so that you can view the other options
- Workflows: If documents created would have the same name as an existing document in the same folder, the name has a number appended to make it unique (like all non-workflow operations already behaved)
- Workflows: Fixed out of memory error when running workflows which produce multiple documents
- Workflows: Fixed sequences not being extracted using Extract Sequences By Name when the names to extract are on new lines
- Workflows: Fixed crash sometimes when selecting a custom icon
- Workflows: Now available from the toolbar by default
- Set Paired Reads: Fixed icon incorrectly showing inwards pairs when used on existing paired reads with different orientations
- General: Fixed crash in some situations when out of disk space
- General: Fixed crash when deleting a folder at the same time as a sub-folder
- General: Added warning before pasting more than 1 million characters in to various text fields (may cause hang)
- General: Proxy settings should update now when proxy.pac changes
- General: Fixed opening links to files in Finder (Mac OS X)
- General: Fixed crash sometimes when attempting to change your data location to a read only folder
- General: Expand/collapse buttons no longer disabled when showing read-only options (eg. from History and Operations table)
- General: Added parent/descendant information to documents produced by Annotation Generators (Mask Alignment and Codon Optimization tools)
- General: Icon or text shown next to cursor when moving documents and folders by drag and drop
- General: Confirmation about erasing all deleted items on startup no longer disappears
- General: Importing folders now asks before re-using an existing folder and defaults to creating a new one
- General: Tips are now shown while Geneious is loading instead of when there isn't a document selected
- General: Further improvements of fonts in Tutorial/help panel and in other components for HiDPI displays
- Text View: When viewing nucleotide quality scores over 99, these are now clipped at 99 in order to make the text view readable
- Shared Database: Fixed a crash that would occur when running a BLAST search from a read-only folder
- Clean Install: Fixed an incorrect message about 'Geneious Education plugin not installed' sometimes after changing your data location to a different drive from the Welcome to Geneious dialog.
- Fasta Import: Fixed crash sometimes when importing amino acid and nucleotide fasta files together
- FastQ Import: Fixed out-of-memory error produced when importing corrupted GZip FastQ files
- GFF Import: Fixed document size after importing wrongly appearing as much smaller than it really is
- GFF Import: When import fails due to invalid characters, the importer will now mention what those chracters are
- GFF Export: Fixed frame/phase being lost when exporting
- SAM/BAM Export: Added option whether to export reads in alignments that don't map to the reference sequence
- SAM/BAM Import: Show warning message when input reads are outside the reference sequence
- GenBank Import: Fixed error that would occur importing documents with "bp", "aa" or "rc" in their names
- Codon Optimization: Fixed crash with some sequences that should be rejected for having ambiguous bases or gaps
- Primer Design: Updated Primer3 to version 2.3.7 see the release notes for more information.
- Tutorials: no longer display wrong images when two tutorials use the same image file names
- DNAStar Import: Fixed a bug that caused import to fail on files containing an empty line between the feature table and sequence
- NEXUS Import: Fixed null pointer exception when parsing files with a DATA block when taxa in trees and alignment don't match
- PIR/NBRF Import: Fixed crash when attempting to identify a nearly empty FASTA file
- Vector NTI: Fixed a crash when importing amino acid sequences with parent/child relationships
- Lineage View: Fixed bug where parent lineage information from some operations was lost after restarting Geneious
- Keyboard Shortcuts: No longer allows setting ALT key shortcuts that don't work because they are assigned to menu items
- Wrapper Plugins: Fixed crash when selecting a folder rather than a file as the wrapper plugin executable
- Biocode Plugin: Fixed crash when pressing the shortcut key to edit a property of a document in the document table when nothing is selected
- Annotate from database: Added option to disable merging of matches with the same type and region
- Agents: No longer available from the toolbar by default or from search options, but are still available under the View menu. Can be added back to the toolbar via right-click on the toolbar
- Tutorials: Now support https links
- Tutorials: Built-in tutorial has been completely rewritten
Other Notes:
- Geneious now requires Java 8 and will no longer run on earlier versions of Java (including legacy Java for Mac OS). This means Geneious will no longer run on
platforms where Java 8 is unsupported such as Mac OS X 10.6 (Snow Leopard) and 10.7 (Lion)
- Geneious is no longer supported on 32 bit Linux
- Geneious has been updated for the NCBI's transition to HTTPS
Patch 10.0.1 (27 September 2016)
Fixes and Minor Changes:
- Restriction Cloning: Various usability improvements and bug fixes
- Workflows: Added 'Randomly Sample Sequences' workflow for randomly sampling (without replacement) a specified number of sequences from a list
- Workflows: Added 'Copy Document(s)' bundled workflow which can be used as part of variant finding workflows to prevent annotating of the input reference sequence
- Workflows: Extract Sequences by Name: Added option to extract each set of sequences that match a specified partial name to a separate document
- Workflows: Fixed crash when using copy/paste on steps in a workflow
- Workflows: Fixed being unable to run workflows with assembly steps with custom trim options
- Workflows: Workflows hidden from the drop down menu are now able to be included as steps in other workflows
- Workflows: Fixed bug preventing running of workflows with an export step with an exposed option for the folder to export to
- Workflows: Fixed crash trying to set export options for SAM/BAM format
- Workflows: Fixed crash after running a workflow step that actively links documents and later modifying one of the input documents. Workflows now no longer attempt to actively link documents
- 3D Structure View: Fixed a crash that would happen on some documents
- Tree View: Made support values near the root end up in correct positions after re-rooting a tree
- Sequence/Alignment View: Right click within a sequence no longer automatically selects the entire sequence when nothing is selected. Added a popup menu option to select the entire sequence
- Sequence/Alignment View: Right click menu 'Add Annotation' is now enabled when nothing is selected to allow creation of annotations between positions
- Sequence/Alignment View: Fixed mouse cursor getting stuck on a busy cursor sometimes when saving
- Sequence/Alignment View: Turning off the checkbox to show any annotations no longer turns off the annotate and predict checkboxes (e.g. Find ORFs or Find Restriction Sites)
- Sequence/Alignment View: Fixed bug where pressing Enter in the annotation filter box prompted to edit the sequence name
- Sequence View: Fixed crash when displaying 3-letter amino acid codes
- Sequence View: Fixed zoom to selection not zooming in enough sometimes when wrapping is on
- Sequence View: Alt-dragging over the origin of circular sequences now zooms to that region correctly
- Alignment View: Fixed copy annotations in selected region to another sequence wrongly disabled
- Alignment View: Fixed out of memory or poor performance copying annotations between reference sequence and consensus in a large contig
- Contig View: Fixed poor performance when deleting regions of large contigs
- Circular Overview: Fixed incorrect editing results after setting a sequence as circular and using undo
- Circular Overview: Alt-left mouse drag now zooms to the selected region
- Circular Overview: Fixed crash and/or wrong sequence showing on genome sequence lists
- Circular Overview: Fixed inaccurate green box which indicates the currently displayed region
- Transfer Annotations: Transferred annotations that extend beyond the aligned region of the annotated sequence and the reference will now be truncated (does not apply to circular alignments)
- Annotate From Database: Annotations with multiple intervals that cross the origin can now be used to annotate similar regions on other sequences
- Wrapper Plugins: Fixed crash when adding new files while renaming the plugin
- Document Table: Fixed Paste Without Annotations for all Sequence Lists
- 16s Biodiversity: Added an upper limit of 500 characters for the job description, longer descriptions submitted from previous versions will be truncated
- Mask Alignment: When creating a new alignment with sites removed, sequences are no longer renamed by default
- Mask Alignment: Saving a new document with sites removed now works when multiple documents are selected
- Map to reference: Fixed mapping reads to all locations sometimes not mapping gappy reads to all inverted repeat regions
- Map to reference: Fixed discovery of incorrect structural variant insertions around repeat regions
- Map to reference: Fixed so that structural variant junction IDs don't skip some values (i.e. they are now numbered consecutively starting from 1)
- Map to reference: Structural variant deletions are now represented as reads with gaps rather than split reads for deletions up to the maximum of 1000 bp or the maximum read length, whichever is larger
- Map to reference and de novo assembly: Made it faster
- Trim Ends: Fixed progress not moving and cancel not working when running slow trimming operations (e.g. primer trimming)
- De novo assembly / Map to reference: Fixed rare crash in some situations
- BBTools: Upgraded to version 36.32
- CloneManager CM5 Importer: CloneManager-specific annotation types have been replaced with standard Geneious annotation types
- Lineage View: Fix end index being off by two when linking a reverse direction child to its extraction parent
- Ligation: Fixed bug where sequence lists couldn't be ligated
- Similarity Search: Fixed crash when there is an alias in a folder being searched
- Paste with Active Link: Fixed so that it works correctly in conjunction with 'Copy (reverse complement)'
- Extract with Active Link: Fixed bug where an extraction was not actively linked if the extraction started and finished at the ends of the source sequence
- Parent/Descendant View: Now correctly updates linked intervals when a parent document change is propagated to a child
- Chimera Filtering: A notification that the USEARCH version is not supported will now be displayed if Remove Chimeric Reads is run with USEARCH v9
- Chimera Filtering: Added SILVA to the list of reference databases
- Chimera Filtering: Made UCHIME failure messages a bit more user friendly
- Primer Design: Fixed crash when running Test with Saved Primers with reverse complementary forward and reverse primers
- General: Fixed memory leak of up to 2 MB per operation run
- General: Fixed crash when dealing with invalid imported protein sequences
Other Notes:
- The Geneious Software License Agreement has been updated. You can access the most current version through Geneious by going to Help -> Online Resources -> License Agreement
Patch 10.0.2 (4 October 2016)
Fixes and Minor Changes:
- Primer Extension: Fixed direction of restriction site annotations
- Convert to Oligo: Fixed crash when run on a sequence list
- Set Data Type: Renamed to 'Set Read Technology'
- Find Variants/SNPs: Fixed crash in rare situations when limiting variants to annotations of a particular type
- Circular Overview: Viewport indicator corners are now always drawn at 90 degrees
- Transfer Annotations: Fixed bug where similarity wasn't always calculated properly for circular alignments with sequences beginning at different indices
- Copy Annotations: Fixed bug where if some tracks were off, it could crash or copy annotations from the wrong track
- Delete Annotation: Fixed crash in rare situations when choosing to also delete an associated annotation
- Restriction Cloning: Changed minimum restriction enzyme recognition sequence length for enzyme sets from 4 to 5
Patch 10.0.3 (18 October 2016)
Fixes and Minor Changes:
- Annotation Table: Table can now be exported in tab separated values (TSV) format
- Annotation Table: Fixed commas not being stripped from numbers before export
- Map to reference / de novo assembly: Fixed crash in some situations when data contains non-N nucleotide ambiguities
- Cloning: Fixed broken lineage for cloning operations after importing documents
- Cloning: One-Line warning in cloning options is more informative
- Restriction Cloning: Fixed broken lineage when re-running an operation after changing the underlying sequence
- Restriction Cloning: Fixed bug where the terminal ends on circular products weren't updated correctly
- Restriction Cloning: Fixed failing digestions if the product is linear and a terminal reaction is on a circular sequence
- Restriction Cloning: Fixed warning that indicated that an additional cut site was outside chosen cut sites but which was actually internal on inserts that span the origin of a circular pre-digested fragment
- Golden Gate: Fixed crash when running the operation using pre-digested sequences
- Golden Gate: Fixed crash when running an operation that requires PCR on a sequence that uses exactly one primer with an existing overhang extension
- Find Restriction Sites: Fixed bug where in some cases restriction sites were not found
- Updated NCBI BLAST databases
- NCBI: Fixed problem accessing https sites such as NCBI when via a web proxy
- Tree builders: Fixed NPE when cancelling a tree inference with the 'Mask Alignment' option checked
- Tree builders: Fixed NPE when building tree on sequence lists imported from fasta format
- Mask Alignment: Fixed bug where progress could appear to go backwards if stripping a mask in a track with a very large number of intervals
- Workflows: Fixed crash (or text being drawn in wrong location) when viewing a workflow that contains a workflow which contains custom Java code you didn't write yourself
- Workflows: Fixed crash when attempting to use copy/paste shortcut keys on steps in a workflow, this is now disabled
- Sequence/Contig View: Fixed crash when using annotation filter while a trim annotation is selected
- Transfer annotations: Fixed crash when running on multiple documents
- VCF Export: Fixed genotype being ignored when exporting
- Plugin Development: Fixed crash moving documents to a hidden folder in a shared database
Patch 10.0.4 (25 October 2016)
Fixes and Minor Changes:
- NCBI: fixed failing downloads of full sequences due to missing GI numbers
- Restriction Cloning: Fixed various crashes involving circular sequences with no restriction enzymes available for digestion
- Restriction Cloning: Fixed a crash when running the operation on some sequence types
- File menu: change order of items in the menu to be the same as before R10
Patch 10.0.5 (26 October 2016)
Fixes and Minor Changes:
- Map to reference (and possibly other operations): Fixed crash in some situations
Patch 10.0.6 (23 Nov 2016)
Fixes and Minor Changes:
- Restriction Cloning: Fixed bugs where base insertions/deletions couldn't be propagated if they changed the position of the used restriction sites
- Restriction Cloning: Fixed bugs where changes couldn't be propagated correctly if an input sequence had been reversed in the options
- Restriction Cloning: Improved performance when using large enzyme sets or long insert sequences
- Golden Gate Cloning: Fixed crash that could happen when designing primers for restriction sites over the origin of a vector
- Cloning: Fixed crash when running 'Digest into Fragments' or Restriction Cloning that occurred as restriction sites were sorted
- Sequence View: Fixed occasional crash when copying tooltips
- Lineage View: Fixed the region of sequence that the lineage applied to being lost after using 'Save As'
- Lineage View: Fixed a problem where changes to the links between documents were not saved between runs of Geneious
- Primer Design: Recompiled primer3 for 32-bit Windows
- Primer Testing: Fixed primers being annotated on the wrong sequence when reordering and deselecting the sequences while primer testing is running
- Extract PCR Product: Fixed bug that caused parent/descendant intervals to not be updated when modifying sequences that have had PCR products extracted
- NCBI BLAST: Fixed situation where Hsps with higher BitScore but same E-value as the lowest Hit weren't included
- NCBI BLAST: Fixed situation where updates to the Blast url in properties.txt were ignored
Patch 10.0.7 (14 Dec 2016)
Fixes and Minor Changes:
- BLAST: Fix problem not creating reference back to query in hits returned from Custom BLAST tblastn, and creating incorrect reference for tblastx
- BLAST: Fix problem not returning the best Hsps when there were fewer Hits than specified in Max Hits but more Hsps
- BLAST: Fixed annotations that were in the wrong direction when running tblastx that returns a result with a negative query frame
- Annotation Filter: Fixed numerical comparisons failing when an annotation has a range of values (e.g. 'coverage>70' would not match an annotation with a coverage value of '80 -> 85')
- Fix incorrect warning when running under Red Hat Enterprise Linux
- Agents: Fix a crash that occurs when right clicking in table of Agents
- Map to reference / de novo assembly: Fixed failure to align sequences containing an ambiguity (e.g. N) to other sequences containing the same ambiguity
Geneious Server:
- Custom BLAST: Fixed problem getting results from tblastn and blastx running on Geneious Server
- General: Fix problem causing Geneious clients to load documents unnecessarily i.e. when running operations on documents that reside on the Geneious Server and also not viewing them on the client
Patch 10.0.8 (18 Jan 2017)
Fixes and Minor Changes:
- Lineage Operations: Fixed issue where Extract PCR Product would fail to find primers when rerun in some situations
- Map to reference: Fixed crash when discovering structural variants on a circular sequence when there is an inversion and another structural variant near the origin
- De novo assembly: Fixed crash sometimes when assembling sequences containing N
- NCBI Blast: Added WGS Human database and possibility to blast against other specified WGS databases
- Geneious msi installer on Windows: Fixed issue that double-clicking a .geneious file would launch Geneious without importing the file
Patch 10.0.9 (25 January 2017)
Fixes and Minor Changes:
- NCBI Blast: Fixed failure to connect to NCBI server (400) when downloading protein sequences after changes by NCBI
Version 9.1 (2 February 2016)
Patch Versions:
9.1.1
9.1.2
9.1.3
9.1.4
9.1.5
9.1.6
9.1.7
9.1.8
Features:
- Alignment View: Uses colors from Tree View as the background color for each sequence
- Alignment/Contig View: Added option to ignore ambiguous disagreements when highlighting or using 'go to next disagreement'
- Alignment/Contig View: Added option to skip to the next column when using 'go to next disagreement'
- Alignment/Contig View: Made it possible to go to next or previous disagreement in current sequence or reference sequence only without using shortcut keys
- Text Importer/Exporter: Geneious can now import, store, display, and export plain text and html files
- NCBI: Added hyperlink to Pubmed articles
- Gibson Assembly: Added ability to chose exonuclease activity to enable operations such as SLIC, SLiCE, CPEC, InFusion and GeneArt Seamless Cloning
- Map to reference: Added workflow to map multiple sets of reads to their corresponding reference sequence with the same name or name prefix
- Lineage View: More information about operations is now shown in the parent and descendant trees
- Lineage View: New "Save as HTML" button to save parents and descendants as bullet points for reporting
- CRISPR Site finder: Now accepts sequence lists and groups of sequence documents, allowing for batch discovery and scoring of CRISPR sites
- UniProt: Updated search fields to better match the options available on the website
- General: Added ability in Operations table to display the options used for a running operation
- General: From operation options dialogs, can set keyboard shortcut and/or add button to toolbar to run the operation in future
- General: Operations without icons are now able to be added to the toolbar by right clicking on it or from a button in preferences
- General: Further improvements for larger font sizes and HiDPI displays
Fixes and Minor Changes:
- Annotate from database: Restore defaults button no longer restores the folder to its default value. The folder can be restored to its default value independently from the folder chooser
- CSV/TSV importer: When importing to a list, the document name created now matches the imported file name
- CSV/TSV importer: Can now import huge files using very little memory
- Map to reference: Fixed crash choosing an empty folder as reference sequence
- Map to Reference: Fixed crash when input reads are modified while mapping is in progress
- Map to Reference: Fixed crash selected a folder containing a mixture of lists and stand-alone sequences as reference sequences
- Startup: Fixed crash on startup when Geneious does't have permission to write to your Geneious data location
- Startup: Fixed crash during FlexNet installation on some windows systems
- Find In Document: Now ignores leading and trailing spaces on the text to find
- Sorting documents: Fixed rare crash when sorting by a column that contains a mixture of numbers and non-numbers
- Sequence View: Improved sorting of sequences within a sequence list so that names with numeric values are sorted numerically
- Sequence View: Fixed hang on very large sequences when viewer panel is resized down to less than 4 pixels wide
- Sequence View: Uses OpenSans font bundled with Geneious on all platforms. By using a known font, text can now be better positioned so it looks much nicer
- Sequence View: Improved rendering of text in circular views so that it is more readable and also text is no longer drawn upside down in the lower half of the view
- Sequence View: Fixed rare crash when editing primer annotations
- Sequence View: Fixed double clicking to edit an annotation not working if you click near the right-hand side of the annotation
- Sequence View: Fixed crash changing annotation generator settings while generated annotations from another tool are selected
- Sequence View: Fixed problem where mouse cursor could disappear when running BLAST while viewing a circular sequence
- Sequence View: Fixed crash sometimes when printing or saving to an image after turning off all annotations
- Sequence View: Fixed crash sometimes when selecting a region outside the bounds of a circular sequence when it is in a list containing longer sequences
- Sequence View: Fixed crash attempting to 'apply selected annotations' when the same document has unsaved changes in a different window
- Sequence View: Change Residue Numbering on linear sequences now skips zero when including negative numbers
- Alignment View: Stopped it adding (modified) to alignment name when just editing annotations
- Contig View: Fixed crash in rare situations when editing a contig
- Contig View: Fixed reads not showing up sometimes when printing or saving to image
- Find Variants/SNPs: No longer filters variants due to strand-bias near of the sequenced region for paired reads. Previously this logic only applied near the ends of the reference sequence rather than the sequenced region.
- Find Variants/SNPs: Fixed crash or wrong results if the reference sequence is not the first sequence in an alignment or contig
- Save image as PDF: Fixed so that shaded annotations look correct
- RaxML: Consensus support values are now shown by default and can be displayed on branches
- RaxML, FastTree, Garli, BBTools: Documents produced now have the same description as input documents
- Document Table: don't automatically add "modified" to names of documents
- Golden Gate: Complementary primers get created at nearest cut site instead of at the sequence end
- Golden Gate: Creates 20bp primers by default if using primer extension and warns user if the sequence is shorter than 40bp when not using existing primers
- Golden Gate: Fixed crash showing options from history of imported assemblies
- Golden Gate: Fixed crash showing options from history when some of the documents with primers have been deleted
- Golden Gate: Fixed incorrect overhang handling for pre-existing overhangs
- Golden Gate: Fixed enzyme cut sites being introduced when creating random overhangs
- Golden Gate: Show warning if pre-existing overhangs are different to the overhang created by the selected enzyme
- Golden Gate: Warning correctly shows the actual overhang instead of always the overhang on the top strand
- Toolbar: Fixed bug where items would sometimes go missing from the toolbar after customizing the items to display
- Enzymes: Avoids crash on startup if a previous download of the enzyme set was not successful
- SAM/BAM Export: Improved performance
- Local BLAST: Include BitScore value in the result document fields
- BLAST: Fixed crash or wrong sequences being searched when there are unsaved changes and it prompts to save when you click BLAST
- BLAST: Changed NUM_ALIGNMENTS to 1000 (as response to this post) instead of to the value given in Maximum Hits
- NCBI: Fixed DBSOURCE and DBLINK fields not being added to GenBank documents
- NCBI: Fixed an infrequent bug where certain old GenBank documents had annotations that would cause the indexer to crash
- Gibson Assembly: Fixed crash when performing the operation on some documents
- VCF Exporter: Fixed allowing any IUPAC ambiguous bases instead of just N
- VCF Exporter: Fixed crash when cancelling export during sequence track loading step
- Workflows: Show warning if options have changed that make the workflow invalid
- Tree View: Fixed hang that could occur when viewing large trees with their branches ordered. Improved overall performance on these trees
- Tree View: Fixed crash that could happen when indexing a database with a tree document with a small, negative branch length
- Shared Database: Fixed a problem that would cause the database to deadlock and cancel operation when multiple users add and edit documents in the same folder at the same time
- Document Viewers: No longer allow documents to be modified in document viewers if they have an operation running on them
- GFF Import: Fix wrong value in error message when lengths don't match and add sequence names to the error message when they also mismatch
- GFF Export: Fixed when Export to strict GFF, certain character get escaped when it shouldn't according to GFF format standard
- Primer Testing: Fixed an issue where a large amount of memory was being unecessarily used when generating mismatch annotations.
Testing with mismatches should now use a lot less memory
- Phylip Import: Fixed crash when importing file when some sequences appear to be probably nucleotide and others appear to be probably amino acid. The sequence type is now guessed by consider all sequences together
- Lineage view: added additional information to 'Extraction' and 'Digest into Fragments' operations
- Spreadsheet Importer: Now accepts carriage return-only line endings, which Google Sheets outputs
- Batch Rename: No longer displays preview when being run from a workflow. In many cases the preview would not contain the correct values
- GFF Import: Fixed the issue by putting the correct error/warning message to recognise empty GFF file and a GFF file without annotations
- BED and GFF Importer:update the error message on importing the attached GFF file (with the FASTA) which contains duplicate sequences
- Linux: Fixed crash on startup on Linux systems that don't support custom cursors
- Feature Finder: Fixed a crash that occurs if searching large contig assemblies for a subset of features in a folder
- Extract PCR product: Fixed a bug where Parent Descendant propagation would fail on sequences lists with only one sequence
- De novo assembly: Fixed case where 'minimum overlap' setting was not respected
- General: Fixed a crash that occurs when deleting multiple folders with the same name
- Vector NTI: Fixed a failure to link parents and descendants when importing Vector NTI Advance archives with custom enzymes
Patch 9.1.1 (23 February 2016)
Fixes and Minor Changes:
- Data Location: Warns that if you set your Geneious data location to a Google Drive, OneDrive, iCloud Drive, or DropBox folder, it could cause data loss or crash Geneious if these don't completely synchronize before you use Geneious from another location
- Keyboard shortcuts: If you try to assign a new shortcut already assigned to something else it now removes the shortcut from the other action after warning about it
- Fasta Import: Fixed failure while importing UTF-8 BOM encoded fasta file
- Mean Coverage: Fixed mean coverage in document table incorrectly handling trimmed regions in some cases
- Sequence View: Fixed width of sequence track "Options" button on Mac OS X
- Sequence View: Increased default annotation thickness in circular views
- Sequence View: Fixed annotations coming back after restart if all are deleted from NCBI gene documents
- Sequence/Contig/Alignment View: Fixed occasional crash
- Sequence/Contig/Alignment View: Fixed text inside annotations extending outside the ends of the arrows sometimes
- Sequence/Contig/Alignment View: Fixed images next to names, graph scale bars and graph heights for HiDPI displays
- Sequence/Contig/Alignment View: Fixed crash in rare situations on MacOS after ctrl-clicking
- Contig View: Fixed annotations spanning the origin of the reference sequence in a circular contig not being rendered near the start of the sequence
- Contig View: Fixed clicking RNA seq / structural variant link sometimes appearing as fewer than three fading gaps even when there are at least 3 trimmed nucleotides
- Contig View: Fixed deleted trim annotations sometimes reappearing after saving
- Contig View: Fixed bug where trying to create undirected annotations on circular contigs would create directed annotations instead
- Map to reference: Fixed paired read handling when spanning large deletions or introns where it would sometimes incorrectly trim the entire read due to wrongly thinking paired reads overlap
- Map to reference: Fixed crash sometimes when finding structural variants when mapping to a circular reference sequence
- Map to reference: Fixed structural variant mapping annotations not appearing sometimes
- BBTools: Upgraded to version 35.82
- Ace Import: Improved the message displayed when the imported file has certain errors
- SAM/BAM Import: Fixed poor performance and excessive memory use when importing RNA seq data with large introns or DNA data with large deletions. Large introns/deletions are now annotated during import with reads spanning them split into 2 parts with hyperlinks between them.
- GFF Import: Fixed crash when importing files that don't quite adhere to the GFF format (e.g. GFF files exported from earlier versions of Geneious)
- Import: Fix poor performance or out of memory crash when importing a pair of large files
- Find CRISPR Sites: Fixed crash that could happen when running CRISPR on sequences with unsaved changes
- Improved Splash-screen and other icons for HiDPI displays
- Nexus/Newick Exporter: Branch length will be exported as Standard Numeric format now rather than in a Scientific notation
- Save as Image: Fixed crash that could happen when exporting very large images as JPEG
- Primers: Fixed crash that could happen when designing for a region entirely beyond the end of a sequence
- Licensing: Geneious will now correctly check the expiry date of subscription licenses when checking for new versions
- Licensing: Fixed incorrect warning displayed for certain subscription licenses saying they are not valid for current version
- Spreadsheet Importer: Can now import .TSV files of the kind that Google Sheets exports
- Spreadsheet Importer: fixed a couple of bugs relating to documents of various charsets not importing high unicode characters properly
- Always extract primer sequence for mismatching primers while extracting PCR product for list of sequences or multiple sequences
Patch 9.1.2 (1 March 2016)
- NCBI BLAST: Changed BLAST to request results after 5 seconds when NCBI estimated time remaining is unreasonable
Patch 9.1.3 (5 April 2016)
Fixes and Minor Changes:
- BLAST: Prevent results from different searches being delivered to the same folder for UniProt/Swiss-Prot
- BLAST: Prevent results folder from being deleted when a search is canceled if the folder already contains data
- BLAST: Fixed a problem that caused BLAST hits to be exported in a format incompatible with previous versions of Geneious
- Consensus Tree Builder: Fixed crash that could happen on trees with no branch lengths
- Sequence/Contig/Alignment View: Minor improvements to make nucleotides/amino acids appear less blurry
- Sequence/Contig/Alignment View: Fixed so that trim annotations are the same thickness as they were before 9.1
- Sequence/Contig/Alignment View: Trim annotations are now hidden by default in all views except on a single sequence or pairwise contig
- Sequence/Contig/Alignment View: Fixed hang sometimes when selecting a region in the consensus on very high coverage contigs
- Sequence/Contig/Alignment View: After editing an annotation, fixed rare situation where clicking may crash or not select the next annotation clicked on
- Contig/Alignment View: Fixed potential loss of saved changes when applying changes to referenced sequences while running low on free memory
- Contig View: Fixed rare crash when viewing some contigs at a zoom level close to the point where it hides reads when zoomed out too far
- Contig View: Fixed crash if you set a paired read as the reference sequence and choose link paired reads in the layout options
- Sequence View: Fixed crash when viewing circular chromatograms
- Sequence View: Fixed excessive reloading of viewer and potentially lots of 'too many tracks' dialog messages when calculating expression levels
- Circular Contigs: Fixed so that reverse complementing a circular contig gives correct results now
- Circular Contigs: When editing a circular contig with a reference sequence to insert ot remove gaps from the reference sequence, the circular contig length now updates correctly
- Circular Contigs: If you change the reference sequence and extract that sequence, the extracted sequence is no longer incorrectly marked as circular
- Sequencing Preferences: Increased the maximum allowable values for medium and high quality base coloring thresholds from 99 to 30,000
- Save as EPS/EMF format: Fixed crash or bad looking images when 'Shaded annotations' option is on by disabling the option for EPS and EMF formats
- Map to reference: Fixed bug where it would unnecessarily introduce gaps sometimes
- Map to reference: Fixed crash sometimes when the option to find structural variants is on
- Map to reference: Fixed incorrect mapping quality in some cases
- De Novo Assembly: Fixed wrongly showing warning sometimes about too many contigs when assembling fewer than 100 sequences
- Find Repeats: Fixed crash sometimes when allowing a high percentage of mismatches
- Start up: Fixed crash on startup on some Windows systems when trying to access a data location on an unreliable network drive
- Start up: Improved start up behaviour when previous data location is not there. It now always prompts to choose a data location in this situation and won't allow you to pick an invalid location
- General: Fix some text areas not being adjusted for larger font sizes and HiDPI displays
- EndNote import: Prevent it from attempting to import unrecognized xml files
- Trim by Vector: Fixed a problem where operation would continue in the background when cancelled
- Geneious Server: Fixed bug where if the input documents to an operation were in different folders, the input documents would be copied into the destination folder
- Save As will no longer move documents between folders if the original folder is not selected
- Contact Support: Fixed problem where pressing enter in the message field could send the message unexpectedly
- Cloning from Workflows: Fixed crash when running a restriction cloning from workflow with inserts with two annotated cut sites
- Fasta Import: Fixed a problem where auto-detect did recognise FASTA file if whitespace appeared in the first sequence
- CSV/TSV Import: Fixed the preview becoming too wide for the import options window
- Gibson Cloning: Fixed bug where it could not propagate changes on imported documents that involved a Gibson Operation
- Gibson Cloning: Uses origin of the backbone if it's an extraction that contains the origin
- Tree View: Fixed crash that could happen when filtering nodes in a tree while applying actions to that tree
- Shared Database: Minor improvements to prevent duplicate search index in shared database
- Extract PCR Product: Now keeps all primer bind annotations in the product, instead of discarding those not used for the extraction
- NCBI Search: Fixed so that when NCBI has internal server errors they are reported instead of returning no results from the search
- Fixed a bug where new installations of Geneious wouldn't remember existing proxy server preferences
- Trees: Fixed a crash that would occur when swapping taxon names in some tree documents
Patch 9.1.4 (10 May 2016)
Fixes and Minor Changes:
- Workflows: Fixed so that dissolve input contigs setting is available when configuring assembly workflows instead of the workflow silently using the most recently used value for that setting. This setting is now on by default, means that any existing workflows which assume it is off will need to be reconfigured
- Workflows: Fixed bug preventing 'Combined Mapping and De novo assembly' workflow from being run
- Workflows: Fixed bug preventing 'Set CDS translation property' workflow (and any other custom code workflows with inner classes) from being run sometimes
- Workflows: Trim and Filter workflow on paired reads filters both reads if either read in the pair matches the filter criteria, and fixed unfiltered reads to remain paired
- De Novo Assembly / Map to Reference: Fixed bug introduced in 9.1.3 causing a crash in some situations
- Iterative Map to Reference: Fixed bug causing incorrect alignment when reads overhang the ends near regions of no coverage. Also slightly better results in other iterative mapping situations
- Map to Reference: Fixed paired reads sometimes using a non-optimal alignment when they align to repetitive regions
- Contig View: Fixed crash in some situations after clicking cancel when asked whether to apply changes to original sequences
- Remove Duplicates: Fixed to operate on each input sequence list independently instead of all lists combined
- PCR Product Extraction: Fixed a bug where sometimes the wrong primer was used if two primers were at the same interval
- Blast: Fixed crash that could sometimes happen when downloading multiple full sequences that are grouped into frames
- Blast: Removed '(Frame null)' that was sometimes appended to the query name in the query-centric view
- General: Fixed rare crash that could happen at any time
- General: Fixed rare crash that could happen when trying to browse for a file on Windows
- Geneious Tree Builder: Fixed a bug where annotations in tracks on sequences in an alignment were lost through tree building
- Tree View: Max chars for tip labels can now go up to 9,999
Geneious Server:
- Custom BLAST: Fixed maximum hits option incorrectly being limited to 100
- Drop support for RHEL/CentOS 5 and Java 6. Run under Java 8
Patch 9.1.5 (13 June 2016)
Fixes and Minor Changes:
- Map to Reference: Fixed crash or sub-optimal results on some data sets when using iterative mapping
- De Novo Assembly Report: Contig statistics (e.g. N50) now use ungapped contig lengths instead of gapped contig lengths
- CAP3 De Novo Assembly: Fixed to save all contigs generated by CAP3 rather than just the first one
- NCBI: Show error message if sequence is incompletely downloaded due to a slow internet connection
- BLAST: Some results folders would fail to load with a crash if Geneious lost track of the query
- BLAST: Fixed wrong annotations that would happen with the new XML2 format returned by NCBI Blast if a reverse hit is found
- Trim ends: Fixed VectorScreening options to match up with NCBI's vecscreen tool
- Large protein sequence lists: Fixed crash when working with these from some operations such as workflows or InterProScan
Geneious Server:
- Work around bug in new release of tomcat that prevented serving of some web pages by Geneious Server
Patch 9.1.6 (20 September 2016)
Fixes and Minor Changes:
- Contig View: Fixed bug where changes to annotations in consensus sequence tracks would be discarded when saving in some situations
- Sequence View: Fixed shift-selecting between two restriction sites selecting wrong region for restriction sites that match the reverse strand
- Collaboration: Fixed a crash that would happen when connecting/disconnecting to a newly set up account for the first time or connecting to more than one account
- Workflows: Fix icon size increasing after each save of a workflow when using a HiDPI display on Windows or Linux. This would eventually result in Geneious running out of memory
- DevKit: Fix incorrect property in copyPluginAndRename ant task in some of the example plugin build configurations
Other Notes
Geneious Server:
- Fix deletion of local temporary file directory when Geneious Server runs no operations for over 24 hours that could cause some operations to fail
- Fix duplicate results folders created when source and target are both on shared database
- Fix race condition that could lead to incorrect job count preventing any new jobs from running
- Fix errors in Geneious Server log file when edits are made to shared database metadata, such as when users share workflows
Patch 9.1.7 (22 November 2016)
Fixes and Minor Changes:
- NCBI: Fixed problem accessing https sites such as NCBI when via a web proxy
- NCBI: Fixed failing downloads of full sequences due to missing GI numbers
- NCBI Blast: Fixed situation where updates to the Blast url in properties.txt were ignored
- Tree View: Made support values near the root end up in correct positions after re-rooting a tree
Other Notes:
- The Geneious Software License Agreement has been updated. You can access the most current version through Geneious by going to Help -> Online Resources -> License Agreement
Patch 9.1.8 (14 February 2017)
Fixes and Minor Changes:
- NCBI: Uses Accession.Version numbers rather than GIs (GI numbers are being phased out by NCBI)
- NCBI Blast: Fixed failure to connect to NCBI server (400) when downloading protein sequences after changes by NCBI
- Tree View: Fixed possible crash when incorrect preferences are saved
- Custom BLAST: Update executable files for 32-bit platforms to their respective latest valid release
Version 9.0 (1 September 2015)
Patch Versions:
9.0.1
9.0.2
9.0.3
9.0.4
9.0.5
Features:
- Golden Gate - one step cloning of large constructs using any mixture of inputs with existing cut sites or automatically designed primers
- RNA-seq and structural variant mapping - Map to reference can map to existing annotated coding regions or discover novel introns and fusion genes during mapping.
For DNA sequencing, the mapper can discover structural variants and annotate them. This also allows correct alignment of the ends of reads around deletions and structural rearrangements
in heterozygous samples
- VCF export - supports exporting single-sample variants
- Tadpole - very fast de novo assembler with very low mis-assembly rate
- Support for huge phylogenetic trees:
- Greatly improved performance, both when loading and rendering trees
- New search box for finding nodes and taxa
- New automatic collapsing of sub trees based on distances
- CRISPR:
- New scoring strategy for on-target activity, proposed by Doench et al 2013
- Options to control how many mismatches and indels are allowed when scoring against off-targets
- The target sequence can now be inside the off-target database and will be scored accurately
- Improved performance
- Read filtering:
- Merge paired reads using BBMerge
- Error correction and coverage level normalization using BBNorm
- Duplicate read removal using BBDedupe
- BBDuk plugin for additional trimming (provides adapter, paired read overlap, quality, minimum length, and entropy trimming)
- New plugins available for download:
- BBMap mapper for DNA/RNAseq
- EupathDB for searching and retrieving eukaryotic pathogen sequences
- Repeat Finder for annotating all regions that are repeated elsewhere in a sequence
Minor Features:
- Map to Reference: Can choose multiple reference documents from options
- Map to Reference: Automatically soft trims regions of a paired read that extends back past the start of its mate
- Map to Reference: Added option to only map paired reads when both reads in the pair map somewhere
- Variant Finding: Added option to exclude reads not near their expected distance from variant finding calculations
- Fasta Export: Added ability to exporting paired reads to parallel fasta files
- Print / Save to Image: Added option to turn off yellow box around reference sequence
- Workflows: Added option to save to a sub-folder name that depends on document names from an earlier step in the workflow
- Workflows: Added 'List all sequences with variants' workflow that lists the names of all sequences that contributed to at least one variant
- Workflows: Added 'Batch Restriction Cloning' workflow for inserting each sequence into the same vector
- Workflows: 'Add document chosen when running workflow' step now supports select any sequence from anywhere in your database from inside the options
- Workflows: 'Extract Sequences by Name' now has an option to extract the inverse instead
- Workflows: Can export documents to external files as a step in a workflow
- Workflows: Rename step can now form document names based on up to two documents from previous steps in the workflow
- Workflows: Added checkboxes to hide shared and sample workflows from the workflow management list
- Assembly Results: The restore defaults button no longer resets checkboxes in the results section. And sub-folders results appear bold until they have been viewed
- Assembly Name: Can add variables that are replaced by the values of particular settings. The assembly name setting has its own restore defaults button
- Assembly/Mapping/Variant Calling: The name of the reads mapped or assembled is added as a field on contigs produced. Variant calling uses this to form the default track name
- Variant Calling: Includes the name of the CDS annotation as a property called "CDS" on each variant
- Sequence/Alignment/Contig View: Annotations have clickable links in their popup text to select and zoom to each interval
- Sequence/Alignment/Contig View: Added checkbox to (de-)select all annotations & tracks at once
- Sequence/Alignment/Contig View: 'Go To Position' sequence name/range can be empty to mean all sequences. For example ':500-600' will select columns 500 through to 600 in an alignment
- Sequence/Alignment/Contig View: Added modifier keys to next disagreement/gap/ambiguity button to only find matches in the currently selected sequence
- Sequence/Alignment/Contig View: Renders trimmed regions faded when zoomed out
- Trim by Vector: You can now select Custom BLAST databases as vector databases, and annotate trim regions from multiple databases at a time
- Shared Database: Restricted license now allows read-only access to shared database server
- Primer Design: Improved the speed on larger sequences when a target region and product size range have been specified
- Wrapper Plugins: Added support for creating Java based wrapper plugins. See help button next to command line options in wrapper plugin creation interface for details
- Distances Matrix: Added option to display similarity percentages on protein alignments (using Blosum matrices)
- NCBI Gene and SNP Documents: Annotations in tracks can now be added to NCBI gene/SNP documents
- Administration: Can disable installation of plugins and workflows with custom code by editing geneious.properties in the Geneious install directory
- Batch rename: Added the ability to rename fields of documents with annotation qualifier values
- Operations such as BLAST and Alignment can now be run from secondary windows via the menu
- Import Directory: New menu operation to import a file directory tree, copying the directory tree structure as child folders
- GFF Import: Added support for importing tracks from Ensembl
- Improved support for larger font sizes and HiDPI displays
- Golden Gate: Fixed some annotations not being truncated when extending over the origin of circular sequences
Fixes and Minor Changes:
- Reverse Complement: Fixed so that paired read orientations are correct after reverse complementing a sequence list
- Extract & Translate buttons on annotations from multiple alignment documents shows message to perform the action from the Tools menu instead
- Field values that are changed from the document table now actually show what is wrong if it doesn't match the constraints
- Sequence View: Fixed crash in rare situations when clicking on an annotation
- Sequence View: When extracting undirected annotations, these can now be concatenated
- Sequence View: Fixed crash when you have hundreds of annotation types or tracks
- Sequence View: Fixed hang or poor performance viewing some circular sequences with annotations with many intervals
- Sequence View: Fixed crash when there is not enough free memory to load a large sequence list
- Sequence View: Fixed hang in rare situations when using find dialog
- Sequence View: Fixed crash in rare situations when saving changes
- Sequence View: Fixed hang or poor performance viewing annotations with names or properties millions of characters long
- Sequence View: Fixed so that when extracting a subset of sequences from a list of paired reads, the paired reads are kept in the original order
- Sequence View: Fixed crash when reordering tracks when the same document has unsaved changes in a separate window
- Sequence View / Annotations Table: Fixed hang or poor performance working with annotations which have long html qualifiers
- Sequence View: Fixed hang sometimes when you click cancel to give up on slow saving of large images
- Sequence View: While drag selecting a region, the status bar now updates to reflect what is currently under the mouse
- Sequence View: Fixed poor performance zooming in/out on annotated sequence lists of hundreds of thousands of sequences
- Sequence View: Fixed crash in rare situations when scrolling horizontally at the point where it requires vertical scrollbars to be introduced
- Annotations Table: Fixed bug when more than one alignment/contig is selected, the values min (original sequence) and max (original sequence) could sometimes be incorrect
- Alignment/Contig View: Fixed rare situation where when the start of a read was outside the visible range, the entire read would not appear
- Alignment/Contig View: If consensus sequence is turned off, it is no longer calculated in the background
- Alignment/Contig View: Fixed situation where it would sometimes tell you to zoom in to view reads when it shouldn't be necessary to
- Alignment/Contig View: Fixed poor performance / hang when sequence logo graph is turned on for long contigs with regions of very high coverage
- Consensus Options: Added help button that quotes relevant section from the manual about how the consensus threshold works
- Keyboard Shortcuts: Disabled keyboard shortcuts with just shift as a modifier as these generally don't work and can cause crashes
- Map to Reference: Fixed crash when input documents are modified while mapping is in progress
- Map to Reference: Added explaining 'Help' entry & label to clarify reads and references
- Map to Reference: Improved performance creating results from mapping to large reference sequences
- Assembly: Pressing Esc in options dialog now cancels the operation (like it does for all other operations)
- De Novo Assembly: Fixed bug where 'paired hits left' in progress message could be negative sometimes. This same bug also caused de novo assembly to be a bit slower than it needed to be due to calculating some things twice
- De Novo Assembly: Fixed bug where it would fail in rare situations with an error message about begin unable to create a contig containing just one sequence
- De Novo Assembly: Fixed so that if 'Only use paired hits during assembly' is used on paired data and next time de novo assembly with unpaired data, the setting is turned off and disabled so that assembly still proceeds
- Fixed poor performance (or hangs) copy lots of annotations between sequences on large alignments/contigs
- Extract Annotations: enabled for consensus sequences of alignments
- Annotations Table: can now extract annotations on consensus of alignments
- Annotate From Database: Fixed crash that could happen occasionally when transferring primer bind annotations
- Export with Parent/Descendants: Fixed crash exporting documents that are their own parent or descendant
- Concatenate Sequences: Improved performance when concatenating thousands of sequences
- Workflows: Fixed 'Align DNA via Muscle, Clustal and Geneious' to work on sequences that are not already grouped into a list
- Workflows: Fixed 'Extract Sequences By Name' to work on also match reverse complemented sequences (those with " (reversed)" appended to their name)
- Workflows: Fixed to fail with a graceful error message instead of crashing when a custom Java code workflow returns null from performOperation
- Search Index: Variant annotations are no longer indexed in database to improve performance
- Search Index: Fixed crash when running low on memory
- Startup: Fixed crash on startup sometimes when connected to a shared database
- Shutdown: Fixed poor performance/hang during shutdown sometimes
- Change Data Location: Fixed broken images in various locations after moving your Geneious data location from preferences
- Topo Cloning: Fixed bug in annotation handling for circular sequences
- NCBI Search: Gets documents according to NCBI's 'relevance' sorting
- NCBI Search: Fixed a bug where the options would crash on certain contigs with certain consensus options selected
- NCBI Search: Fixed a crash that occurred sometimes when a running search's folder was deleted
- NCBI Search: Fixed a crash that occurred sometimes when NCBI returned invalid data
- BLAST: Fixed a problem where annotations on hit sequences did not transfer over when creating an editable copy of the query centric alignment
- Tree View: Fixed shifting node attribute values when a conceptually unrooted tree is manually rooted
- Tree View: Fixed a crash that could occur sometimes when manually rooting a tree at an external node
- Tree View: Fixed a hang that could occur when manually rooting a large tree
- Proxy settings: Fixed an issue where Geneious was defaulting to Direct Connection mode when the Use Browser Settings option was selected
- MacOS and Linux: Fixed crash sometimes when out of file handles due to Geneious keeping too many files open
- Strip Alignment Columns: Added a setting when stripping alignment columns to limit the maximum number of extraction intervals. This will alleviate memory issues when both creating and viewing the stripped alignment
- Extraction: fixed a bug where extracting a subsequence would sometimes not respect the option to exclude intersecting annotations
- Fixed a bug where double clicking on a file with Chinese or other high-codepoint characters in the path would not get imported when Geneious started up
- Dropbox: Fixed crash when you have partially synchronized your data with Dropbox and DropBox has created "conflicted copy" files in Spanish in your Geneious database. Using Dropbox like this can lead to data loss so we strongly advise against using it. Also fixed identical crash when using other unknown file synchronization software that creates conflicting copy files
- Data Location: Fixed bug where if you change your data location from the welcome dialog, sometimes the old data location is recreated with a few enzyme files in it
- Shared Database: Fixed poor performance sometimes working with chromatograms grouped into a list
- Shared Database: Removed unnecessary warning about not being able to modify documents when running operations from a read only folder
- Enzyme Table: Fixed bug when sorting values where some are empty
- Jmol: Fixed a crash when viewing some molecules from the Sequence View
- Export: On Windows the drop down list of file types available for export to no longer has scrollbars after just 10 file formats
- SAM/BAM import: Fixed incorrect results and/or crash when importing a mapping to a circular reference sequence
- SAM/BAM import: Fixed poor performance importing files which used = where there was a match to the reference sequence
- SAM/BAM import: Fixed crash when attempting to import corrupt BAM files. Now fails with a nice error message instead
- Workflows: Fixed a crash that can happen when exposing some boolean options in workflows
- Workflows: No longer keeps all intermediate documents in memory while running workflows, so it is now feasible to run workflows on very large data sets
- Geneious Server: Fixed crash when trying to run an assembly on Geneious Server with a blank name
- CSV Export: Can now include document URN
- CSV Export: Improved memory usage
- CSV Import: Added support for quoted new lines in values
- Lengths Graph: Fixed hang when Lengths Graph window was made small
- General: Fixed occasional problem were if the file system encounters an error, Geneious would silently ignore it and continue as if it had worked
- General: Stopped Geneious grinding to a halt sometimes when it is running low on memory
- General: Fixed occasional crash when running backup, changing data location, or shutting down when connected to a shared database that contains shared workflows
- Backup: Now remembers the last location you backed up to on shutdown
- Move Folders: Fixed crash sometimes when moving lots of folders at once
- Options dialog: Fixed issue where warning labels would disappear when options are reset to defaults
- Primer3: Fixed a bug where primer3 couldn't open Unicode file paths on Windows, meaning that primer3 couldn't run when Geneious was installed under a Unicode directory on Windows
- Primer design: Fixed a crash when attempting to assign probe penalty weights when not designing a probe
- Add 5' extension: fixed slowness with the Add Restriction Site combo box, and slowness with combo boxes elsewhere in Geneious. Also made it so that only commercial enzymes show up in this combo box
- Newick Tree Importer: Fixed bug that could occur when Newick files have metacomments or illegal characters in taxon names
- Newick Tree Exporter: Exporting trees with metacomments will more accurately choose the metacomment to export on internal nodes
- Fixed a crash related to invalid document fields such as those that can be generated by the Moorea Biocode
plugin when switching between different FIMS
- CRISPR Site finder: Will now handle multi-interval selections and extractions better with a slight speed up
- CRISPR Site finder: Will no longer return CRISPR sites that are over the boundaries of selections
- CRISPR Site finder: Will no longer return pairs of CRISPR sites that pair over the boundaries of selections
- CRISPR Site finder: Can now pair CRISPR sites without having to go through off-target scoring
- CRISPR Site finder: When the target sequence is inside the off-target database, the tool will now inform the user of where it was found and how many copies there were
- Gibson Assembly: Fixed crash when propagating changes when a vector is removed from a sequence list
- Ligate Sequences: Primers and Restriction Sites are not removed when they extend into an overhang
- GFF Import: Fixed a problem where annotations would incorrectly be grouped together into a single multi-interval annotation if they had the same qualifiers and no ID
- GFF Import: Fixed a problem where the frame for multi-interval CDS was being read from the wrong interval if it was reversed
- GFF Import/Export: Improved handling of invalid and escaped characters
- Newick Import: Now auto-detects .nwk
Other Notes:
- Geneious no longer requires legacy Java 6 from Apple, Oracle Java 8 is now bundled. A distribution that uses legacy Java 6 is also available for older machines, however, this will be discontinued for R10
Patch 9.0.1 (22 September 2015)
Fixes and Minor Changes:
- Map to Reference: Fixed crash with RNA seq or structural variant discovery in some cases
- Map to Reference: When dissolving an existing contig and remapping, fixed 'Reads Name' assembly name property to correctly use the original reads name
- Map to Reference: Fixed occasional crash and occasional failure to map reads when sequencing reads are longer than a circular reference sequence. Long reads are now split into multiple fragments in the results
- Find Variants and Compare expression levels: Fixed very slow performance in some cases when calculating p-values
- Find Variants: Fixed crash merging adjacent variants when sequencing reads are longer than a circular reference sequence so that individual reads can contribute two different variants to a single position in the reference sequence
- Contig View: Trimmed regions when zoomed in with the paired distance color scheme and now rendered in grey
- Workflows: When workflows create copies of sequences for their results, custom notes from the input sequences now appear on the output sequences
- Workflows: Fixed occasional crash when changing your data location
- Sequence Extraction: Genetic code is now copied from source sequence into extracted sequence
- Contig/Alignment View: Fixed complement rendering in wrong location if both complement and translation are turned on when translation is set to only show on consensus and/or reference sequences
- Sequence ligation: Ligating chromatograms with large sequences (over 100,000 bp) now discards chromatogram information from the results to prevent poor performance
- Parts of a primer extension can now be removed via a delete button on each part
- Extract PCR Product: Now retains annotations on primer extensions if you extract the primers from the pcr product
- Extract PCR Product: Results now show original numbering on primer extensions relative to the extraction rather than the extensions themselves
- Extract PCR Product: Fixed a bug where original numbering would not be set when the PCR product covered the whole sequence
- Golden Gate: Extensions added to existing primers are no longer saved on original primer
- Golden Gate: Improved parent descendant handling
- Golden Gate: Fixed bug where it didn't update the vector correctly when some options were changed
- Golden Gate: Adds enzyme annotation to extracted primers
- Golden Gate: Added possibility to choose between multiple primers
- Golden Gate: Update button is stateless and updates only when clicked
- Mac OS: AppNap and sleep are now prevented when Geneious is running an analysis or importing or exporting (only on Mac OS 10.7+ with Java 8)
- Large trees: Fix out of memory error when indexing large tree documents present in your database
- Tree View: Fixed bug where an options panel was disappearing whenever a tree was modified and saved
- Tree View: Fixed bug where autocollapse subtree options were not updating after re-rooting a tree
- Tree View: Fixed a bug where the tree view would freeze Geneious at certain zoom levels and auto collapse settings
- Fixed a crash if Geneious could not create a new database on upgrade
- CRISPR Site Finder: fixed bug that allowed it to annotate groups of Ns as valid CRISPR targets
- BLAST: Fixed a bug where occassionally the full sequence was downloaded rather than just the specified hit context
- Alignment: Fixed a problem where Geneious would hang when showing the options for re-aligning a large alignment
- Start up: Fixed Geneious occasionally failing to start on 32 bit operating systems
- Rename Folder: Fixed so that you can change the capitalisation of a folder name
- VCF Importer: Fixed bug where multiple samples were being collapsed into one track
Patch 9.0.2 (7 October 2015)
Fixes and Minor Changes:
- Contig View: Trim annotations are now off by default on large contigs and reference mappings. When trim annotations are off, trimmed regions are shown as strikethrough text
- Annotate from database: Includes annotations from tracks on sequences in database. Added option to only include specified annotation types. Added option to exclude specified annotation types
- RNA Seq / Structural Variant Mapping: The track created is now only visible by default on the contig it corresponds to and off when viewed from other contigs
- RNA Seq / Structural Variant Mapping: Fixed crashes in some situations
- RNA Seq / Structural Variant Mapping: Fixed failure to run when 'Assemble each sequence list separately' is on
- MacOS and Linux: Fixed crash sometimes when out of file handles due to Geneious keeping too many files open
- Info View: Fixed incorrect error message about failure to save sometimes and crash soon afterwards
- Fixed a crash that would occur if switching to the data storage location to a path ending in whitespace
- VCF Importer: Changed the single sample naming scheme to use the imported file's name
- 32 bit operating systems: Fixed Geneious occasionally failing to start and/or occasionally crashing later during normal usage
- Viewer preferences are now remembered when a new window is opened
- Split views are now remembered when switching between documents of the same type
- Extract PCR Product: Now correctly moves annotations in sequence tracks to account for any primer extensions
- Set Paired Reads: When selecting multiple lists for batch pairing with variable length names, it now recognizes pairings when the forward/reverse variable character is before the last character and after the variable length position. e.g. A_1_F_001, A_1_R_001, A_2_F_001, A_2_R_001, A_10_F_001, A_10_R_001
- Options dialogs: Basic options will have a scrollbar now and advanced (more) options will have appropriate size for better accessibility
- BBTools: Upgraded to version 35.49 and added PacBio mode checkbox to BBMap
- Tree View: Expansion slider is now relative to the size of the tree so it can go high enough on huge trees and it stays consistent when switching between trees
- Tree View: When there are more than 1,000 labels visible at once then they are all hidden to improve performance
- Tree View: Many other improvements to rendering performance on huge trees
Geneious Server:
- Removed SAMtools variant finder plugin from server. Uninstall the plugin from Geneious and use Geneious variant finder instead
Patch 9.0.3 (3 November 2015)
Fixes and Minor Changes:
- Local Documents: Fixed bug where if you view the contents of a folder while hundreds of documents are being added to it, some of those documents might not appear until you restart Geneious
- Annotate from database: Include/Exclude types now matches on prefixes rather than the full annotation type text. This setting also applies to gateway annotations now
- Annotate from database: Multi-interval undirected annotations are now supported as long as the intervals are ordered in the forward direction
- Tadpole: Fixed crash when attempting to run tadpole on data which contains a read which is 0 bp long
- Plugins: Plugins installed without administrator preferences are now installed to a location outside of your Geneious data location
- Windows: Fixed some plugins failing to work after changing data location
- Windows: Fixed crash changing Windows display settings while viewing operations table
- Linux: Fixed flickering that would occur when performing some actions
- Empty values in Meta-Data and New Sequence now show placeholder text on Mac OS
- Workflows: Fixed bug introduced in 9.0.1 where only the first workflow change made after starting Geneious is saved.
- Workflows: De novo assembly in a workflow can now configure the maximum number of contigs to generate and can configure it to use a subset of the full data set
- Sequence Logo: Fixed crash on alignments with over 100,000 columns
- Sequence/Alignment/Contig View: Improved performance when saving to PDF/SVG
- Alignment/Contig View: Fixed incorrect translation of consensus sequence after editing but before saving
- Alignment/Contig View: Fixed incorrect translation frame when translating in frame of the consensus or reference sequence when it does not begin at the start of the alignment or around regions with gaps in both sequences
- Alignment/Contig View: Fixed shadow under viewers top panel on long sequences
- Contig View: Fixed incorrect rendering of trim sequences in circular contigs
- Contig View: Fixed clicking RNA seq / structural variant link sometimes not jumping to the destination position in the contig
- Contig View: Fixed clicking RNA seq / structural variant link sometimes not appearing as three fading gaps
- Map to reference: When mapping an alignment to a reference sequence, sequence descriptions and properties are now preserved in the generated contig
- Structural Variant Mapping: Fixed crash in some situations
- Structural Variant Mapping: Added 'Rearrangement Distance'/'Fusion Distance' properties to annotations
- Structural Variant Mapping: Improved detection of structural variants when there are nearby SNPs
- De Novo Assembly: 'Assemble each list separately' setting can now be used in conjunction with 'Use X% of data' setting
- Find Variants/SNPs: Fixed incorrect p-value calculation on merged variants in regions of high coverage
- Fixed situation where some Linux distributions are unable to open clickable URLs within Geneious
- GenBank Flat Importer: Now imports files correctly when qualifier values contain / characters
- OneDrive: Fixed crash when you have partially synchronized your data with OneDrive and OneDrive has created conflicting files in your Geneious database. Using OneDrive (or any other file synchronization software) like this can lead to data loss so we strongly advise against using it
- Dialogs: Improved buttons and icons for HiDPI displays
- CRISPR Site Finder: Fixed problem where input RNA sequences would be scored as DNA when off-target scoring
- CRISPR Site Finder: Fixed issue where CRISPR couldn't be run on some sequence lists, saying the target sequence was too short
- CRISPR Site Finder: Fixed crash that could happen when an off-target database contained alignment documents or trees
- CRISPR Site Finder: Will now run to completion on sequence lists when one sequence has no CRISPR sites, instead of cancelling early
- Tree View: Fixed a problem where the Automatically Collapse Subtrees slider displayed the previous value rather than the current value
- Tree View: Fixed a problem where the Automatically Collapse Subtrees slider would ignore changes on small trees
- Tree View: Prevent the viewer hanging when viewing large trees with the Species Delimitation plugin installed
- Tree View: Fixed inverted "Too many labels to display" warning
- VCF Export: Added ability to export sequences as FASTA alongside VCF export
- VCF Export: Fixed option to export original source being incorrectly enabled by default
- VCF Import: Fixed source data files not being added correctly in some cases
- UniProt: Fixed problem when search with multiple terms with a Match 'ALL' statement is returning results as Match 'ANY' statement
- CSV/TSV Spreadsheet-Sequence importer: Fixed crash which happen in rare situations when importing document with CSV/TSV importer
- Sequence View Controls: Improved buttons to support larger font sizes and HiDPI displays
- Annotation generator: Fixed memory leak caused by real time annotation generator progress bar
Patch 9.0.4 (5 November 2015)
Fixes and Minor Changes:
- Fixed issue that prevents activation of licenses for first time users on Mac OS
Patch 9.0.5 (14 December 2015)
Fixes and Minor Changes:
- Plugin Table: Improved for HiDPI displays
- Improved dialog layout when clicking "More Options" or "Show Details"
- CRISPR site finder: Fixed crash that could happen when scoring against an off-target database that includes protein documents
- CRISPR site finder: Fixed crash that could happen when using a circular sequence with a selection starting at the origin
- Keyboard Shortcuts: Run on incorrect documents after editing workflows or changing data location
- Workflows: Can now configure trim step to remove existing trim annotations
- Tree View: Will not clip collapsed node labels off the edge of the default tree view anymore
- Tree View: Will not lay out space for labels when there are too many labels to display
- Tree View: Collapsed node labels will be colored by the color of the node, or black by default, and line up properly with branches
- Tree View: Collapsed node labels will use the same names as Tip labels, instead of the default taxon name
- Tree View: Disabled Species Delimitation plugin on large trees by default. This can be turned back on using advanced options
- Contig View: Fixed clicking RNA seq / structural variant link sometimes not jumping to the destination position in circular contigs
- De novo assembly: Fixed crash or slightly wrong results in rare situations
- Assemble by name or by sequence list: Contig names now respect the assembly name setting unless saved in a sub-folder
- Shared Database: Fixed a deadlock that could occur if documents are added to a folder at the same time as documents inside the folder are being saved
- General: Fixed hang sometimes when doing a full backup of your Geneious data
- General: Fixed crash when running an operation from a secondary window when there is no sequence/alignment view
- GTF Importer: Fixed bug where multi-interval annotations on the reverse strand were imported with intervals in the incorrect order
- Cloning: Fixed crash on overhangs with more than one interval
- Variant Finder: Fixed crash sometimes analyzing effects on translation when there are multiple variants within a single codon
- SAM/BAM export: Fixed crash when exporting over approximately 700 million sequences to a single SAM/BAM file
- NCBI: Download of WGS sequences now downloads all sequences mentioned in WGS & WGS_SCAFLD into a sequence list
Version 8.1 (10 February 2015)
Patch Versions:
8.1.1
8.1.2
8.1.3
8.1.4
8.1.5
8.1.6
8.1.7
8.1.8
8.1.9
Features:
- Batch Primer Design: Design primers for many regions within a single sequence in one step
- Vectors and inserts can now be chosen from different folders after opening "Gibson Assembly"
- Reference sequence can now be chosen from a different folder after opening "Map to Reference"
- FreeBayes Variant Finder Plugin (64 bit platforms only)
- Contig/Alignment View: Added option to only show translation on consensus and reference sequences
- %GC: All newly created nucleotide alignments, contigs, sequence lists, and sequences have a %GC field in the document table. Sequences in alignments, contigs and lists can be sorted by %GC
- Mapping Qualities: Geneious mapper produces mapping qualities, SAM/BAM import/export handles mapping qualities, Contig View displays mapping quality in status bar, added mapping quality color scheme, variant finder takes mapping qualities into account when calculating variant p-values
- Export Documents: Documents can now be exported in the compressed .fasta.gz and .fastq.gz formats
- Export Tree documents: Export to newick format may now include supporting values
- Import speed and memory usage has been improved for very large trees
- Shared Database: Admin users can now specify a compatibility version that will determine the format used to save documents in the database
- Geneious documents and files can now be opened by clicking a link in web-based systems (Windows and Mac OS only) - see Administration section in user manual
Minor Features:
- Compare Expression Levels: Added log ratio, normalized transcript counts, and normalized TPM as properties for each gene
- Sequence View: Added checkbox to 'find in sequence' dialog to disable finding the reverse complement too
- Primer design and testing now have an option to match each sequence in an alignment (instead of just the consensus)
- De novo assembly and map to reference: Better results on data with gappy error models (e.g. Ion Torrent data)
- Annotations Table: Added a right click popup menu to allow copying the selected value, extracting, translating, showing on sequence, editing, and deleting
Fixes and Minor Changes:
- Windows: Double clicking '.geneious' files now opens them in Geneious
- Fixed bug that wrongly allowed creation of contigs containing a single sequence, which could lead to later crashes
- Improved performance working with databases with thousands of folders
- Improved performance when running low on available memory
- Group Sequences and Extract Sequences: Fixed so that edited field values (e.g. taxonomy) on the source document are correct on the derived document
- Workflows: Fixed translation operation in workflows to translate in frame 1 instead of frame 3
- BAM Import: Fixed excessive memory use and poor performance importing bam files with long reads
- BAM Import: Imports mapped reads without sequence data as a sequence of ambiguous nucleotides (NNN...)
- BAM Import: Fixed crash when importing corrupt BAM files
- BAM Export: Uses read group names with spaces replaced with underscores since some other software can't handle spaces in read group names
- BAM Export: No longer replaces IUPAC ambiguity symbols with N, but also added an advanced option to enable the old behaviour
- De Novo Assembly: 'Use x % of data' setting can now specify values less than 1%
- De Novo Assembly: Stopped it producing circular scaffolds sometimes when the circular assembly setting is off
- De Novo Assembly: Fixed crash in rare situations when producing scaffolded circular contigs
- Wrapper plugins: Added debugging mode to see the exact command being run
- Wrapper plugins: Report progress when importing large results
- Wrapper plugins: Fixed so that help window isn't hidden behind the wrapper plugin window
- Wrapper plugins: Fixed so that it doesn't crash when attempting to import invalid result files into Geneious
- Primer Editing: Fixed crash when attempting to remove the interval from a primer annotation
- Sequence View: Fixed bug when double clicking the ends of an annotation when in editing mode prompts to edit the annotation twice
- Sequence View: Fixed out of memory crash when 'Find All' finds too many results
- Sequence View: Fixed crash sometimes when deleting annotations outside the bounds of the sequence
- Sequence View: Fixed crash when doing a 'Find' while dragging regions or annotations around
- Sequence View: Improved performance viewing intersecting CDS annotations
- Sequence View: Displays translation for every region covered by a CDS annotation instead of not showing translation at all for CDS annotations that intersect other CDS annotations
- Sequence View: Fixed rendering glitches on large circular sequences
- Sequence View: Improved performance and reduced memory usage when viewing lots of sequences (e.g. 100,000 +) extracted as sub-sequences
- Sequence View: Improved performance when extracting a whole sequence from a sequence list (e.g. extracting one chromosome from the human genome)
- Sequence View: Fixed excessive memory usage and improved performance when saving large tracks
- Sequence View: Fixed crash adding annotations to sequences with trim annotations when the complement strand is visible
- Sequence View: Fixed crash changing annotations outside the sequence bounds into primer annotations
- Contig/Alignment View: Fixed hang / poor performance viewing larges contigs that have CDS annotations on the consensus sequence
- Contig/Alignment View: Fixed hang / poor performance viewing translation in frame of consensus on sequences with large gaps
- Contig/Alignment View: Fixed hang / poor performance extending selection with shift-up/down arrow keys
- Contig/Alignment View: Fixed copying text to clipboard on circular contigs which would sometimes copy gaps instead of the selected nucleotides
- Contig/Alignment View: Fixed crash in rare situations when editing contigs with trimmed sequences
- Contig/Alignment View: Fixed crash exporting coverage graph from circular contigs
- Contig/Alignment View: Fixed crash or incorrect paired read handling extracting from a contig when the consensus is also selected
- Contig/Alignment View: Fixed selection message when multiple sequences are selected to count columns rather than an estimate of the number of nucleotides and gaps
- Enzymes View: Disabled on over 100,000 sequences to prevent hangs
- Primer Design: Fixed some crashes on circular sequences when entering an invalid included region
- Conflicting Changes: Fixed rare message about there being conflicting changes when saving a document when there aren't any conflicts
- Digestion Operations: Fixed a possible hang when thousands of sequences should be digested
- VCF Import: Fixed so that meta info and some annotation properties are not discarded in some cases
- Reverse Complement: Fixed crash in rare situations when clicking the 'Reverse Complement' button
- Gibson Assembly: Replace 'Editing History' with 'Gibson Primer Extension' annotation to include it in primer extension
- Gibson Assembly: Using a new document chooser that can remember previously selected vectors
- Custom Blast: Corrected handling of preformatted & custom Blast databases
- Custom Blast: Naming & Accession of Custom BLAST Hits was sometimes incorrect
- Custom Blast: Summaries from workflow can now download the full sequence from its original service
- Dropbox: Fixed crash when you have partially synchronized your data with Dropbox and DropBox has created "conflicted copy" files in your Geneious database. Using Dropbox like this can lead to data loss so we strongly advise against using it
- Expression Analysis: Fixed crash sometimes when running two expression analysis operations simultaneously on the same reference sequences
- Fixed a crash that can occur when the data folder is the root of a hard drive and the user upgrades their Geneious version
- Annotate From and Transfer Annotations: transferred primer annotations are now named for the primer they came from, and include extension information
- Annotate From: Multiple primers with different extensions are transferred as separate annotations, instead of merged into one annotation
- Restriction Enzyme Finder: Disabled unnecessary & buggy range option on multiple unaligned sequences
- Set Paired Reads: Pairing multiple data sets with variable length document names now works (e.g. sample1_R1, sample1_R2, sample2_R1, sample2_R2, ..., sample10_R1, sample10_R2)
- Genome Summaries: Downloads always the newest version
- Tree Building: Fixed crash in some cases when building trees from sequences with duplicate names
- Import tree documents: Fixed a Bug where imported unrooted newick trees might have had the supporting values on the wrong branch
- Create tree documents: Fixed a Bug that might happen when Taxa were named as integer smaller than the total amount of taxa
- Plugin Download: Fixed performance issue so that plugins now download and install faster
- Blast Hits: correct representation of transferred annotations in alignment and query centric view
Other Notes:
- "Download Annotation Tracks" has been removed due to incompatible changes to the data at the Broad Institute
Patch 8.1.1 (24 February 2015)
Bugs Fixed:
- Expression Analysis: Fixed crash when working with data sets where all reads map outside of CDS annotations
- Sequence View: Tweaked so that full names don't pop out until 0.5 seconds after you stop moving the mouse
- Sequence View: Fixed hang when editing lots of trim annotations
- Sequence View: Fixed hang when trimming lots of annotated sequences
- Find Variants/SNPs: When run on multiple contigs, it now prompts whether or not to apply the changes to referenced documents
- Find Variants/SNPs: Fixed so that merged variants which have a range of frequencies state the frequency range instead of just the maximum frequency
- Find Variants/SNPs: Fixed so that merged variant frequencies aren't lower than expected when some reads only partially intersect the variant region
- Find Variants/SNPs: Added "Variant Raw Frequency" property
- Strip Alignment Columns: Fixed issue causing it to create inefficient alignments which would cause the Alignment View to hang on large alignments
- Contig View: Fixed hang sometimes right clicking when a large region (100,000 + sequences) is selected
- Contig View: Fixed crash if you pick black as a paired distance color
- Export: Fixed crash sometimes when exporting documents with parents and descendants
- Export: Reduced size of Geneious format exported documents
- Fixed crash sometimes working with over approximately 250 million paired reads
- Biocode plugin: Fixed PCR plate primers going missing (bug introduced in 8.1.0)
- RAxML, FastTree, Garli: Fixed crash shortly after running one of these for the first time
- Dropbox: Fixed crash when you have partially synchronized your data with Dropbox and DropBox has created "conflicted copy" files in your Geneious database. Using Dropbox like this can lead to data loss so we strongly advise against using it
- Workflows: Fixed crash when running Filter workflow on multiple documents
- Translation: Change translation of ambiguities (e.g. N) to translate as X instead of ?
- Shutdown: Fixed hang sometimes when shutting down Geneious
- Map to Reference: Tophat with Bowtie2 now accepts pre-built bt2 or bt21 index files
- De Novo Assembly: No longer produces circular assemblies sometimes from contigs containing only two sequences
- Lineage: Fixed so that lineage view includes documents selected by the new document chooser introduced in 8.1 for reference assembly, primer design and gibson cloning
- Shared Database: Greatly improved start up time when the database has a lot of folders
- Codon Optimisation: Removed incorrect message being displayed about no results being found
- Codon Optimisation: Now optimises stop codons
- Document Notes: Fixed failures when entering special characters
Patch 8.1.2 (3 March 2015)
Bugs Fixed:
- Bam Import: Fixed tracks on reference sequence getting duplicated after editing the imported contig
- Bam Import: Names of imported documents now include the bam name as well as the reference sequence name
- Contig/Alignment View: Improved handling of annotations on circular alignments so that you can manually annotate regions of sequences that wrap past the origin and the mini-map is correct
- Contig/Alignment View: Fixed misleading #bp message next to the mouse when selecting regions to distinguish between bp and gaps
- Map to Reference: Fixed crash when selecting a sequence search result as a reference sequence
- Find Variants/SNPs: Fixed so that merged variant frequencies aren't lower than expected when some reads only partially intersect the variant region
- Gibson Assembly: enabled assembly using RNA sequences
- Import Fasta: remembers whether to import as alignment or separate sequences when importing multiple fasta files
- NCBI Search: Removed Molecule Type filter because it's not supported by NCBI any more
- Document Notes: Fixed tooltip that sometimes extended outside the monitor
- CRISPR Finder: Fixed problem when run on sequence lists of only one sequence
- Generate Consensus Sequence: Improved performance and fixed occasional out of memory error
- Wrapper Plugins: removes empty additional commands to prevent the command line tool from crashing
Patch 8.1.3 (17 March 2015)
Bugs Fixed:
- De Novo Assembly: Fixed crash sometimes
- General: Fixed crash in rare situations when saving changes to a document
- Startup: Fixed crash on startup after using file synchronization software which creates conflicting files in your Geneious data directory
- Startup: Fixed crash on startup when building search index
- Map to Reference: Fixed crash sometimes if you try to map without picking a reference sequence from the drop down list at the top of the options
- Sequence View: Fixed rare crash when selecting multiple regions
- Contig/Alignment View: Fixed circular alignments to correctly handle annotations in tracks on sequences that wrap past the origin
- Contig/Alignment View: Fixed copying tracks between sequences to exclude annotations that don't intersect the destination sequence
- Annotations Table: Fixed bug where the displayed annotations sometimes don't correlate with the settings for which annotations to display
- Restriction Sites: fixed bug where selected region sometimes couldn't be updated
- Sam Importer: Automatically sets alphabet for additional fasta files to nucleotide
Geneious Server:
- Add support for operations that reference documents in the options
Patch 8.1.4 (8 April 2015)
Bugs Fixed:
- Updated NCBI Gene Search to reflect changes to NCBIs new XML display format for ESummary
- Contig View: Fixed so that when you create conflicting changes to an alignment that references contigs, the references are not lost when saving changes
- Contig View: Fixed crash sometimes after saving an edited contig
- Contig View: Fixed crash if you pick black as an over expected distance color
- Contig View: Fixed crash sometimes if you delete sequences then run something from Annotate & Predict
- Consensus Calling: Takes mapping qualities into account when calculating consensus quality
- Map To Reference: Fixed incorrect mapping qualities in some situations
- Map To Reference: Added option to only map reads that have a minimum mapping quality
- Map To Reference: Fixed crash sometimes when choosing options
- Test with saved primers: Fixed crash if someone deletes a primer from a shared database while you are viewing primer testing options
- Optimize Codons: Fixed crash when run on GenBank sequences and saving results as a new sequence
- Gibson Assembly allows assembly with oligonucleotides
- CRISPR finder: Fixed issue where potential CRISPR sites are sometimes scored against themselves or wrongfully eliminated
- CRISPR finder: Fixed crash that would occur when selecting options from workflows
- Compare Expression Levels: Fixed crash that would occur when selecting options from workflows
- Vector NTI Database importer: Now preserves Vector NTI subset information as a metadata field on each document
Patch 8.1.5 (5 May 2015)
Bugs Fixed:
- Start up: Fixed occasional crash on startup on some Windows systems
- Document Chooser: Fixed crash when picking 'Use Folder' when indexing is in progress
- Contig View: Fixed crash viewing some contigs with over approximately 600 million reads
- Sequence View: Fixed hang or poor performance viewing lists of nearly 100,000 sequences containing reads over 100,000 bp long
- Sequence View: Fixed incorrect selection message in status bar when switching between annotations in the annotations table inside the Sequence View
- Find CRISPR Sites: When scoring CRISPR sites, off-target sites with mismatching PAMs will now be considered in relevant cases
- Blast: Fixed shifted annotations when blast hits are extractions from circular sequences
- Search Index: Fixed crash due to out of file handles when indexing lots of sequence lists
- Geneious Devkit: Fixed an issue where the Eclipse classpath was out of date and didn't contain some of the library jars
- NCBI Search: All NCBI Web services can now be disabled via geneious.properties file without disabling the whole plugin (refer to manual for instructions)
Patch 8.1.6 (16 June 2015)
Bugs Fixed:
- Modified Date: When editing documents, fixed bug where modified date would revert to the created date on some documents
- Map to reference: Fixed iterative mapping causing reads to be mapped offset from where they should be in rare situations
- Find Variants: For deletions over about 100bp, fixed incorrect average quality and p-values
- Find Variants: Fixed bug where variants were not getting merged into longer variants sometimes
- Find Variants: Fixed crash in some situations when working with RNA variants
- Find Variants: Fixed crash when reference sequence has trimmed regions
- Contig View: Hide columns over x% gaps would sometimes hide the wrong column in the right-most 8bp of the contig (the fix only applies to newly generated contigs)
- Alignment View: Fixed 'Pairwise % Positive' value to ignore columns which are entirely gaps
- BAM/SAM Export: Fixed so that template length (TLEN) in BAM/SAM files for right most paired read is negative
- Blast2GO: Fixed crash when you have installed the Blast2GO plugin, created some results using Geneious, and then uninstalled the plugin
- Shared Database / Custom BLAST: Fixed error message about data going missing when trying to view some custom BLAST results in a shared database
- Shared Database: Stopped a crash that occurred when documents could not be cleared from the clipboard
- NCBI Gene DB: discontinued entries can be downloaded and won't be ignored anymore
- NCBI Gene DB: Fixed failing downloads of entries with missing GenomicInfo
- Gibson Assembly: Shows message that operation can't be performed when sequences are too short
- Gibson Assembly: Fixed bug where it couldn't find some of the provided sequences in a sequence list
- GenBank File Import: Fixed cases where fields were not imported if KEYWORDS didn't end with a period
- GenBank File Export: Added option to export sequences with a LOCUS name longer than 16 characters
- CRISPR Site finder: Added help button for inputting the CRISPR motif
- UniVec: Updated the bundled UniVec database to the latest version
Patch 8.1.7 (24 August 2015)
Bugs Fixed:
- Find Variants: Fixed crash in some situations when there are variants on both sides of a gap in the reference sequence
- Custom BLAST: Fixed an issue where a user would be unable to cancel future dialogs warning about short or highly ambiguous sequences
- Custom BLAST: Fixed an issue where BLAST very rarely fails when temporary intermediate files would go missing. Geneious would also warn the user of a potential faulty hard drive in this case, which was wrong
Patch 8.1.8 (24 November 2015)
Bugs Fixed:
- Annotations Table: Fixed bug when more than one alignment/contig is selected, the values min (original sequence) and max (original sequence) could sometimes be incorrect
- Alignment/Contig View: Fixed incorrect translation of consensus sequence after editing but before saving
- CRISPR: Removed Maximum Mismatches and Maximum Indels options. These were inactive in this version and did not affect the numbers used for the off-target scoring. Geneious allows 20% mismatches and up to 10% gaps between CRISPR site and off-target site
- CRISPR: Now only allows gap lengths of 1 between a CRISPR site and an off-target site when scoring. This was set to 3, which proved to be too generous
- GTF Importer: Fixed bug where multi-interval annotations on the reverse strand were imported with intervals in the incorrect order
- Tree View: Fixed incorrect re-positioning of some branch labels after re-rooting a tree
- GenBank Flat Importer: Now imports files correctly when qualifier values contain / characters
- UniProt: Fixed problem when search with multiple terms with a Match 'ALL' statement is returning results as Match 'ANY' statement
- BLAST: Fixed a bug where occassionally the full sequence was downloaded rather than just the specified hit context
- Shared Database: Fixed a problem that would cause the database to deadlock and cancel operation when multiple users add and edit documents in the same folder at the same time
- GFF Import: Fixed a problem where annotations would incorrectly be grouped together into a single multi-interval annotation if they had the same qualifiers and no ID
Patch 8.1.9 (27 September 2016)
Bugs Fixed:
- NCBI: Fixed search indexer crash for some nr Megablast batch searches
- NCBI: Fixed PopSet list downloading too few sequences
Other Notes
Version 8.0 (9 September 2014)
Patch Versions:
8.0.1
8.0.2
8.0.3
8.0.4
8.0.5
Features:
- 16S Biodiversity Tool - Cloud-based tool that identifies high-throughput 16s rRNA amplicons from environmental samples using the RDP database, and visualizes biodiversity as interactive graphs and charts using a secure web viewer
- Sequence Classifier - Taxonomically classifies an organic sample by how similar its DNA is to your own database of known sequences using a BLAST-like algorithm with multiple loci and trees to assist with identification (available as a separate plugin)
- CRISPR Design - Locate potential CRISPR target sites and score them based on off-target sites in any genome
- Improved De Novo Assembly - Longer contig lengths, more accurate results, and can also produce scaffolds
- Restriction Analysis:
- Methylation sensitivity now listed for all enzymes
- Added "Must cut between: (may cut outside)" option when finding restriction sites
- Enzyme list is now automatically updated from rebase
- Workflows:
- Merge overlapping sequences mapped to a reference as long as the overlap size and similarity meet specified thresholds (useful for genome finishing)
- Custom code workflow for extracting sequences from a list or alignment by name
- Split a sequence list into smaller sequence lists
- Add a translation property to all CDS annotations
- New workflow step to extract the reference sequence from contigs or alignments
- Contig Viewing:
- Added option to reverse complement individual sequences within contigs
- Added option to move reads mapped to a reference sequence to a specific position in the contig
- When coloring by paired distance unpaired forward directed and reverse directed reads are assigned distinct colors
- Genetic Codes: Added support for defining your own custom genetic codes (from the cog icon next to the genetic code in the Sequence View)
- Generate Consensus: Added option to split consensus into multiple sequences around regions of no (or low) coverage
- Sequence View: Select some of the annotation results from Live Annotate & Predict before clicking Apply to have only those annotations applied
- Sequence View: Added advanced option in preferences to allow displaying more annotations at once (warning: this can cause poor performance)
- Primer Design: Added Inosine (I) to allowed nucleotides
- Windows / Linux: Added option to let Geneious automatically choose a reasonable amount of memory to use based on your machine's total memory.
- When copying documents between folders there is now an option to "keep both" when a document with the same name exists
Bugs Fixed:
- Fixed slow shutdown of Geneious when a large document is being indexed
- Alignment Editing: Fixed deletion of wrong nucleotide in rare situations when you have the cursor positioned in multiple positions in multiple sequences and press shift-backspace
- Workflows: Fixed so that when operations which save to a sub folder are part of a workflow, they still save to a sub-folder
- Workflows: Find ORFs 'Continue outside sequence' option is now available from workflows
- Workflows: Find Duplicates is now configurable from workflows
- Workflows/Shared Database: Fixed crash on startup in rare situations when workflows are stored in shared databases
- Mapping: Fixed crash mapping to a 0 length circular reference sequences
- Mapping: In some cases gaps near mismatches would be positioned differently for different reads when they could be placed in multiple locations with the same number of mismatches. Now gaps are always positioned as far right as possible
- Sequence View: Fixed poor performance when viewing thousands of unaligned sequences with annotations
- Sequence View: Fixed poor performance / hangs when creating or saving non-trim annotations on large sequence lists
- Sequence View: When finding sequences that occur in millions of locations, warns you before running out of memory or hanging/li>
- Sequence View: Fixed crash when extracting from sequences with large tracks when running low on memory
- Sequence View: Fixed circular sequences with over 500 annotations turned on, so that it now shows annotations spanning the origin when zoomed in
- Sequence View: Improved performance on MacOS and also fixed occasional hang on MacOS
- Sequence View: Fixed poor performance / hangs when a large quantity of text (e.g. 10MB or more) is copied to the clipboard in other applications
- Sequence View: Fixed crash when there are hundreds of different types of annotations on a sequence
- Sequence View: Fixed hang/crash when translating a large list of sequences in all 6 frames
- Sequence View: Fixed bug with circular Sequence View that wasn't always positioning the cursor correctly when running Geneious with Java 8
- Sequence View: Fixed rare crash when drag selecting regions
- Sequence View: Fixed rare crash view sequence list documents with translation turned on
- Sequence View: Fixed rare crash copying selection to clipboard
- Sequence View: Fixed crash after editing multiple annotations in tracks
- Sequence View: Fixed crash deleting lots of selected regions from sequences
- Sequence View: Fixed crash and/or incorrect coloring of heat mapped annotation tracks after manually editing an annotation
- Sequence View: Fixed crash and/or incorrect results after renaming a newly generated track and using the undo button
- Sequence View: GC% being lower than it should be due to gaps and ambiguities being counted as non-GC characters
- Sequence View: Fixed poor performance / hangs when viewing large sequence lists containing circular sequences
- Alignment View: Fixed rare crash when extracting sequences from an alignment
- Contig View: Fixed poor performance / hangs when dragging regions of sequences around in large contigs
- Contig View: Fixed poor performance / hangs when copy annotations to all sequences in a large contig
- Contig View: Fixed out of memory / poor performance / hangs / when turning off nucleotides and names on high coverage contigs
- Contig View: Fixed ugly rendering of consensus sequence when mouse is over the sequence name
- Annotations: Fixed various case sensitivity issues. For example when editing annotation types. And when finding variants where 'cds' annotations were not recognized as 'CDS' annotations
- Annotations Table: The 'Sequence' column for primer annotations shows the primer sequence instead of the region covered by the primer
- Annotations Table: Fixed crash on MacOS sometimes when editing annotations
- Find Variations/SNPs: Fixed crash when ignoring SNPs in annotations that have intervals outside the sequence range
- Extract Annotations: Fixed poor performance and excessive memory usage on large contigs
- Separate by barcode: Fixed out of memory error when separating into hundreds of barcodes each of which has thousands of sequences
- Windows: Fixed crash that can happen when changing Windows theme (or in other situations involving display changes)
- Windows: When installed from the MSI, a running instance of Geneious can be pinned to the taskbar on Windows 7 and Windows 8.1
- Dotplot View: fixed problem with lines getting thinner and thinner until they almost disappeared as you zoomed out
- Text View: Fixed crash sometimes when selecting documents
- Import: Fixed crash sometimes when importing multiple files when one of the files is unable to be imported
- Import: Fixed crash when auto determining the file format of a very large file
- Import: Fixed crash when trying to import a compressed empty file
- Nexus Import: Fixed crash when importing deep nexus trees
- SAM/BAM Import and bowtie running: Stopped Geneious prompting about the sequence type when the reference sequence contains too many ambiguities
- BAM Import: Fixed crash when attempting to import corrupt BAM files
- RAxML: Now works if sequence names contain characters such as brackets
- Group Sequences: Fixed some document types (such as primers) from losing their document type when grouped and extracted again
- Group Sequences: Preserve paired read information when grouping multiple lists together
- Fixed invalid primer type in sample documents
- Extract PCR Product: new documents get the name of the sequences they were extracted from rather than the name of the sequence list or alignment
- Fixed extension options in primer design not remembering their values
- Fix for the deletion of associated annotations
- Primer design on alignments: Now exposes the Sequence View's consensus options for more fine-tuned control of the consensus
- When deleting a primer annotation in a sequence list or alignment, the associated annotations can also be deleted now
- Custom Blast now downloads full hits from the NCBI database if no local database is available
- Fixed crash when out of disk space
- Fixed crash on startup when system temporary directory property is invalid
- Batch rename: Fixed a bug where renaming empty strings as part of a larger pattern wasn't working.
- GenBank exporter no longer creates a blank version field (which caused BioJava to fail)
- Made it easier to track down documents that are causing indexing to fail on a shared database
Other Notes:
- UniVec has been updated
- COGs BLAST has been removed
- Linnaeus Search has been removed
- NCBI Genome service now uses BioProjects to retrieve sequences
- 64-bit versions of EMBOSS tools have been added which includes the dotplot, motif search and back translation
- Three protein analysis tools have been moved to a separate downloadable plugin called "EMBOSS Protein Analysis": Predict Secondary Structure, Predict Antigenic Regions, Predict Signal Cleavage Sites
- Two DNA analysis tools have been moved to a separate downloadable plugin called "EMBOSS Nucleotide Analysis": Search for Transcription Factors, Protein Coding Prediction Graph
- Generate Mutated and Shuffled Sequence operations have been moved to a separate downloadable plugin called "Mutate & Shuffle"
- Genetic Codes: Added NCBI tables 24 and 25
- Stylized DNA Helix Graph: Added option to stop the animation
- Sequence View: "Linear view" option moved to the General options tab
Patch 8.0.1 (30 September 2014)
Features:
- Basic RNA-Seq statistics: Added operation to calculate RPKM, FPKM, and TPM
- Basic RNA-Seq differential expression: Added operation to calculate differential expression between two samples
- CRISPR Site Finder: Added option to find and score paired sites on opposite strands
- Sequence View: Added "Invert Selection" (available from right click menu)
- Tree View: The reference sequence is highlighted in green and not hidden when there are too many labels to show them all
Bugs Fixed:
- MIRA: Fixed crash when turning off the option to save contigs
- Garli: Fixed failure to run when sequence names contain unusual characters
- RAxML and other tree builders: Fixed crash on some data sets
- Contig View: Fixed crash setting reference sequence on a circular contig
- Contig View: Fixed poor performance / out of memory when viewing lots of sequences with CDS annotations mapped to a reference sequence
- Contig View: Fixed crash when running low on memory
- Tree Building: Trees built from alignments with a reference sequence keep the reference sequence in the tree
- Sequence View: Fixed so that it highlights the correct sequence as reference sequence on tree documents
- Sequence View: Fixed poor performance / hangs viewing lots of ORF annotations on MacOS
- Sequence View: Fixed crash when attempting to edit a sequence that has unsaved changes in a separate window
- Sequence View: Fixed crash sometimes when exporting graphs
- Sequence View: Fixed incorrect codon usage statistics when there are overlapping CDS annotations
- Sequence View: Fixed incorrect translations when there are truncated CDS annotations
- Sequence View: Fixed occasional crash when clicking the mouse
- Sequence View: Fixed circular sequences being displayed as linear with default settings when upgrading from 7.1 to 8.0.0
- Annotations Table: Fixed to correctly display properties that have html contents
- Tutorial Document Importer: Preserves the folder structure of the imported tutorial zip file
- Distances View: Fixed it incorrectly reporting 100% identity when two sequences had the same name
- Workflows: Strip alignment columns is now configurable from workflows
- Workflows: Fixed translation operation creating duplicate sequences when used on multiple sequence lists. And improved name of documents produced
- Map to reference: Fixed crash when using 'Only map reads which match nearby'
- Map to reference: Fixed crash when mapping large sequences from GenBank
- Custom BLAST: Fixed crash when adding large sequences from GenBank to a custom database
- Export: Fixed crash when exporting MrBayes documents in Geneious 6.0 format when the MrBayes plugin is not currently installed
- Cloning: Fixed crash in some situations when forwarding changes to descendants of GenBank sequences
- Primer Trimming: Stopped it wrongly finding results with single mismatches when 'Allow Mismatches' is off
- Meta-data: Fixed issue where large amounts of text would cause Geneious to freeze
- Removed link to order Primers from Eurofins MWG Operon in Text View of oligo sequences
Patch 8.0.2 (7 October 2014)
- Sequence View: Fixed crash attempting to extract primers that overhang the ends of the sequence
- Contig View Coverage Graph: Fixed crash and/or incorrect coverage around the origin when viewing circular contigs with trimmed regions that span the origin
- Find non-cutting enzymes: Fixed issue that classed an enzyme as non-cutting if it cut both within and without a selected region
- SAM/BAM import: Fixed crash when importing reads mapped to a reference sequence obtained from GenBank
- Map to reference: Fixed crash and/or incorrect results bug introduced in 8.0.0
Patch 8.0.3 (21 October 2014)
Bugs Fixed:
- Molecular Weight Calculation: Gives accurate weights for DNA and RNA sequences now, including contribution from phosphoribose moieties
- Annotate From: Fixed so that if the sequence to be annotated is shorter than the source annotation, it can still be annotated. Missing regions are treated as mismatches when calculating the similarity.
- Sequence View: Improved annotation rendering performance. Up to 20 times faster in some cases
- Sequence View: Fixed annotation rendering glitch where it wouldn't correctly fill the tips of some annotations
- Contig View: Fixed crash when turning on editing mode on circular contigs
- Alignment View: Fixed crash when viewing some Mauve alignments
- De Novo Assembly: Fixed crash when assembling raw traces without quality information
- Fasta Importer: Fixed crash importing invalid fasta alignments
- Jmol View: Fixed a bug where certain 3d structures would crash on import.
- Compare Expression Levels: Fixed crash when running on data sets that have had 'Calculate Expression Levels' run on only a subset of the reference sequences
- Separate by barcode: Fixed crash in some cases when adding new barcode sets
- Primer Editing: Fixed crash when editing primer pairs transferred between sequences in an alignment
- Custom Blast: Allowing preformatted databases without the .nt. or .aa. suffix.
- Import GenBank files: Fixed a bug where a loci was overwritten by a subsequent one when the last entry before the new loci was a contig element
Geneious Server:
- Fix server side custom BLAST database deleted during server restart under some circumstances
Patch 8.0.4 (4 November 2014)
Bugs Fixed:
- Re-align sequences: Keep previously lost descriptions
- Alignment View: When editing gaps or residues in a sequence with an annotation track, the position of annotations in the track in the referenced sequence are now correct
- Alignment: Fixed failure to align sequences containing inosine sometimes when automatically determining direction
- Contig View: Fixed crash sometimes when viewing circular contigs
- Classify Sequences: Fixed failure to find some distantly related results by introducing a new 'Highest Sensitivity' option that does pairwise alignments against all database sequences
- De Novo Assembly: Fixed crash when assembling raw traces without quality information in rare situations
- Calculate Expression Levels: Fixed so that if some reference sequences don't have CDS annotations, it still runs on other reference sequences from that data set
- Compare Expression Levels: Fixed so that if some reference sequences didn't have any reads mapping to them and so didn't produce contigs, you can still compare expression levels
- Compare Expression Levels: Fixed crash on some data sets and improved performance
- GFF import: Fixed incorrect codon start on reverse directed multiple interval CDS annotations
- Wrapper Plugins (e.g. MIRA, Garli, FLASH): Fixed crash and/or poor performance running with programs that produce excessive progress messages
- Trim and Filter Workflow: Fixed failure on multiple documents when some documents are entirely filtered out
- Fasta Import: Fixed incorrectly importing sequence names that contain two or more | characters
- Primer Operation: Fixed incorrect primer extension when primer had leading bases
- Molecular Weight Calculation: Fixed possible null pointer exception when the calculation is interrupted
- Sequence Search: Fixed crash in rare situations when running sequence searches
- Custom Genetic Codes: Fixed all codons being treated as start codons (e.g. in Find ORFs)
- Find Motif & Dotplot: Fixed bug causing these to occasionally fail to run
Patch 8.0.5 (10 December 2014)
Bugs Fixed:
- Document Table: Fixed crash sorting by URL column
- Fix long delay starting up when using floating license on some systems
- Find Variations/SNPs: Fixed crash in rare situations
- VNTI Import: Fixed failure to import files containing one-line misc feature annotation
- Sequence View: Fixed crash when viewing empty or 1bp sequences with CDS annotations
- Translation: Reverted change introduced in 8.0.1 so that CDS translations after truncated intervals were translated as ??? since we can't be sure it is in the correct frame
- Translation: Improved extraction of CDS annotations with frame slippage so that intersecting CDS annotations without slippage are not annotated as truncated. The effect of this is that the overlapping annotation can be correctly translated too
- Fixed an issue where some restriction site annotations from older versions of Geneious wouldn't get recognised by Digest and would crash
- VCF Import: Fix extra annotations added when importing large size files with more than 200 unique sequences
- Geneious Export: Fixed incorrectly formatted file when exporting sequence lists containing tracks such that importing that file into Geneious R7 or earlier would crash the old version of Geneious
- Custom BLAST: fixed a bug where databases of stand-alone sequences types wouldn't correctly have field values that had been previously overwritten, and have the old values instead.
- Alignment Concatenation: Fixed incorrectly concatenated chromatogram when the sequence is not present in all alignments
- SAM/BAM Export: Fixed incorrect export of qualities exceeding 93 (the maximum supported by SAM/BAM format). It now clips higher qualities to 93
- gff importer: fixed a bug with the where features with long parent names would be incorrectly merged into a single annotation
- gff importer: correctly allow ? values when specifying feature strand
Version 7.1 (4 February 2014)
Patch Versions:
7.1.1
7.1.2
7.1.3
7.1.4
7.1.5
7.1.6
7.1.7
7.1.8
7.1.9
- De novo assembly: Added option to produce circular contigs when the ends match
- De novo assembly: Better results on data with gappy error models (e.g. IonTorrent or 454 data)
- De novo assembly: Reduced size and improved performance on large lists of consensus sequences produced
- Strip Alignment Columns: Add an option to remove columns that contain at least one ambiguity
- Strip Alignment Columns: Add an option to strip two columns per codon
- Extract Annotations: Added options to include upstream, downstream and intergenic regions of matching annotations
- Compare Annotations: Easier to use interface, better results, more powerful options (including 3 way comparison), and results include annotation properties
- Statistics: Added molecular weight of short nucleotide sequences
- Primers can now be ordered from Eurofins MWG Operon via link on the Text View of oligo sequences
- Alignment View: Added option to number bases in the consensus sequence
- Sequence View: Improved performance when scrolling with the mouse wheel
- Sequence View: Displays the name of the track which an annotation is in the popup text when hovering over an annotation
- Shared Database: Added the ability to set the group for new folders to be inherited from the parent folder in
addition to the user's primary group
- SAM/BAM importer: Improved performance
- Tutorials: Import into a sub-folder instead of putting all the files directly in the folder they are dragged into
- Identify Organism Workflow: It also includes the taxonomy fields (where available) on each sequences identified
- Distance matrix: Decimal places option is not available for similarity
- Primer testing: now works on the consensus (in a similar way to designing) when run on alignments and contigs
- General performance improvements
Bugs fixed:
- Read Mapping: Better results in some cases and fixed rare crash when mapping to a circular reference sequence
- Info Properties View: Long values wrap to the next line instead of disappearing off the right hand side of the view
- Alignment View: Fixed crash when saving after changing the genetic code on non-editable alignments
- Sequence View: Fixed poor performance rendering translation when there are translation annotations with lots of short intervals
- Sequence View: Fixed crash sometimes when opening sequence with tracks on it in a new window
- Sequence View: Fixed consensus sequence being assigned quality differently than how the consensus operation assigned quality around homopolymer regions
- Newick Export: Exports multiple bootstrap trees instead of just the first one
- SAM/BAM Import: Fixed failure to import some files which have padded alignments
- Assemble by name: Fixed excessive memory usage leading to out of memory error
- NCBI Blast: Fixed crash when binning into has hit vs no hit when run on sequences in alignments
- Read Mapping: Fixed tracks on input reads not appearing in output contig when mapping to all matching locations
- MUSCLE alignment: Update MUSCLE to version 3.8.425 which fixes problems aligning a long sequence
- Annotation editing: Fixed crash when editing annotations on 0 length sequences
- Annotation filtering: Fixed not equals (!=) clause giving incorrect results
- Internet connection: Switched Geneious to prefer ipv4 to fix internet connection issues encountered by people whose firewalls, virus scanners, or proxy servers don't support ipv6
- Annotate From and Transfer Annotations: 'Translation' properties on the source annotations are removed and replaced with a 'Transferred Translation' property
- Annotate From: Fixed documents becoming excessively large when iteratively transferring annotations by using newly annotated sequences as source sequences for future annotation
- Consensus Alignment: Fixed crash if document is modified while alignment is in progress
- Consensus Alignment: Fixed crash sometimes when run on mixture of alignments and stand-alone sequences
- Variant Finder: If find variants is run when there were unsaved changes on a small contig with paired reads, variants near the ends of the contig were wrongly filtered out due to strand bias
- Extracting sequences: If an identical annotation is present in multiple tracks, it would only appear in one of the tracks in the extracted sequence
- Performance: Fixed occasional hangs and poor performance when local documents contains 100,000+ documents
- Workflows: Fixed failure to compile custom code workflows after Geneious had crashed or locked up earlier.
- Workflows: Fixed crash on some documents when using the 'Filter Documents' workflow step
- VCF importer: Properly support missing data fields
- Annotations Table: Fixed crash sometimes when selecting multiple contig documents
- Extract Annotations: Fixed a bug where the option to only include contained annotations wasn't working correctly.
- Fixed occasional crashes that can happen at any time while Geneious is checking if any new plugins are available.
- Fixed occasional crashes when working with folders with hundreds of documents in them
- Custom Blast: Fixed a bug where Custom BLAST databases could get into a corrupt state if deleted during blast operations.
- Custom Blast: Fixed crash when working with Custom BLAST databases that contain invalid nucleotides in the fasta file
- Network drives: Fixed crash and improved performance if data location is set to a network drive
- Backup: Fixed poor performance when backing up to a network drive (poor performance was introduced in 7.0.5)
- UniProt: Fixed failure to search UniProt databases due to change on UniProt servers
Patch 7.1.1 (26 February 2014)
- Workflows: Fixed crash and/or incorrect results when running trimming workflows on data sets of over 100 sequences
- Sequence View: Fixed status bar displaying the incorrect number of results when running some 'Annotate & Predict' operations (e.g. trimming)
- Sequence View: Now includes annotations between bases that are directly on the end of extracted regions in the extraction (also applies when propagating changes from alignments to referenced sequences)
- Sequence View: Fixed poor performance when saving changes to some alignments/contigs
- Sequence View: When showing the "Bin" field next to the sequence names, the html tags are removed
- Sequence View: Fixed crash when extracting sequences from an alignment after reordering the sequences
- Sequence View: Fixed crash in rare situations when saving changes to contigs containing chromatograms
- Sequence View: Fixed translation by consensus to include translation of sequences that have insertions relative to the consensus
- Sequence View: Fixed hang when finding all occurrences of a very common motif when 'translate by selection' is on
- Insert Sizes Graph: Fixed incorrect results on short contigs
- Compare Annotations: Added trio analysis option to find for example annotations in both sets A and set B, but not set C
- Workflows: Fixed batch rename always renaming the 'Name' field instead of the chosen field when run from workflows.
- Primer Editing: Fixed crash when editing primers pairs so that they overlap each other
- Primer Editing: Fixed crash when editing a primer binding site to lie outside the current binding range
- Sequence Search: Handled an exception caused by GenBank returning data of the wrong type
- Document Table: Fixed occasional crash and/or columns in document table not correctly saving the most recent position and size sometimes
- Startup: Fixed Geneious saying your data location isn't writable if it had failed to write to it during an earlier attempt when out of disk space
- Startup: Fixed crash if you cancel backing up your data when upgrading Geneious
- Startup: Fixed warnings about missing plugin files on Mac OS when starting Geneious from network drive
- Preferences: Fixed preferences getting wiped on shutdown in rare situations
- SAM/BAM Import: Fixed crash when importing some documents
- Genome Search: Returns all genomic sequences from RefSeq that are linked to the organism(s) the search term is related to
- CAF Importer: Added support for paired reads
- CAF Importer: Fixed importing trim-annotations
- DNAStar Importer: Fixed a bug where it would import invalid characters when importing from GenBank-style format sometimes.
- Primer Design: Fixed a crash when trying to design characteristics for an extremely degenerate primer
- Primer Testing: Fixed crash when testing on some alignments
- Batch Rename: Fixed a crash renaming the Description field on Sequence List Documents' individual sequences
- Translate Sequences: Fixed a bug where a translation of multiple annotations with several intervals was sorted in reverse order
Patch 7.1.2 (5 March 2014)
- Workflows: Fixed import/export of multiple workflows that are linked to each other becoming detached
- Sequence View: Fixed hang when shift-clicking to select lots of sequences in large contigs
- Sequence View: Reverse complementing an entire alignment now reverse complements annotations on the consensus sequence too
- Sequence View: Changes made to consensus annotations were lost in some situations when clicking save
- Sequence View: Fixed crash in rare situations when editing alignments or contigs
- Sequence View: Fixed poor performance in some cases when lots of annotations are selected
- Feature Finder: Stopped it rounding of ambiguity matches to the nearest number of whole matches when calculating similarity. Also improved documentation
- Linux: Fixed crash on startup sometimes when system clipboard contains data copied from a Google document
- Gibson Assembly: Fixed failure to run on some documents due to invalid editing history annotations
- General: Fixed crash sometimes when clicking on documents
- General: Fixed hang sometimes when when downloading or moving documents
- Shared Database: Fix user list not being displayed correctly when there is a blank user name
Patch 7.1.3 (20 March 2014)
- Wrapper Plugin Creation: Fixed crash when setting default value for integer options, added inputFolderName variable, and allow executable to be from a bundled sub-folder
- Sequence View: Fixed poor performance or hang when finding variants on large contigs, trimming large lists, or selecting large regions
- Sequence View: Fixed crash when turning a track on/off while the same document has unsaved changes in another window
- Alignment/Contig View: Fixed incorrect statistics and/or crash when selecting a subset of the sequences in an alignment or contig
- CAF Importer (used by MIRA): Fixed hang when importing results when low on memory
- Separate by barcode: Fixed crash when trimming without a barcode
- Workflows: Fixed some assembly, mapping, and extract annotation options being wrongly disabled when configuring it from a workflow
- Fixed a bug with Custom Blast databases where the Accession numbers of hits wouldn't show up.
- Fixed a bug with Custom Blast databases where certain original Geneious names for hit sequences wouldn't get returned.
- SAM/BAM import: Fixed crash importing some files which contain padded alignments
- SAM/BAM import: Fixed import incorrectly aligning some reads in padded alignments that have soft trimming
- Document Table: Fixed rare crash when editing a property of a document
- General: Fixed rare crash that could happen when selecting any folder or performing a sequence search
- Database backup: Fixed a bug that causes Geneious to crash on DB backup on MacOS if the OS creates Files in the DB while the backup is running
- Sequencing Preferences: If you edit a profile it now applies those settings. Previously you had to change the selected profile for the settings to take effect
- Sort topologies: Fixed duplicate topologies generated for unrooted trees. Also problems with applying threshold option
Patch 7.1.4 (8 April 2014)
- Custom Blast: Fixed a bug with Custom Blast databases where the Accession numbers of hits wouldn't show up.
- Custom Blast: Fixed a bug with Custom Blast databases where certain original Geneious names for hit sequences wouldn't get returned.
- Custom blast: Reduced memory footprint of custom blast searches which had gone up in prior versions
- Contig View: Fixed hang viewing large circular contigs with consensus sequence numbering turned on
- Contig View: Fixed crash sometimes when reverting editing annotations
- Consensus Alignment: Reduced memory usage and fixed crash when running low on memory
- Read Mapping: Fixed crash when mapping large sequences or sequences with 100,000+ annotations to a reference sequence
- Assembly: Fixed incorrect handling when a single input document contains a mixture of paired and unpaired reads
- Fixed a bug where Geneious couldn't launch on Windows if the user's Path contained double-quotes
- Annotations Table: Fixed crash when viewing multiple documents with lots of trim annotations
- Backup: Fixed crash sometimes when backing up data
- Realign regions / Concatenate alignments: Fixed crash sometimes when applying either of these to chromatograms
- Workflows: Fixed 'Set Paired Reads' from workflows not respecting the selected options in some cases
- Workflows: Fixed assembly so that all trimming options are avilable when running from a workflow
- Workflows: Removed assembly 'sensitivity may be too high' warning that may show up each time you run a workflow
- Group Sequences / Extract whole sequences: Now keeps custom properties added to the sequences
Patch 7.1.5 (14 May 2014)
- SAM/BAM Import: Fixed incorrect estimate of paired read insert size when there are unmapped reads present
- Export: Fixed crash when exporting some sequence search results in a format compatible with Geneious 6.0
- Fixed occasional crash when clicking on a folder
- Batch Rename: Fixed crash that could happen in rare cases when renaming lots of documents
- Shared Database: Fixed an issue preventing documents larger than 2 GB from being loaded when stored in a PostgreSQL v9.3 database
- Shared Database: Fixed an error that prevented document history from being imported from .geneious files when using certain MySQL versions.
- Cloning: Fixed a bug where Multicassette reactions would crash when a document's Att annotations' names had been changed from their defaults
- Sequence View: Fixed poor performance / hangs when annotating results of "Find All" when there are over 10,000 regions
- Sequence View: Turned on 'Create separate annotation for each interval' option by default since having this off causes performance issues when a single annotation has thousands of intervals
- Sequence View: Fixed crash in rare cases when slow running 'Annotate & Predict' results come back after you unselect the document you ran it on
- Sequence View: Fixed alignment data becoming incorrect in some situations when a sequence list it references has sequences deleted or reordered
- Alignment View: Fixed very poor performance calculating statistics on large protein alignments which could lead to out of memory errors
- Installation: Fixed failure to run when installed to a location that contains a plus sign in the folder name
- NCBI: Fixed a bug where some WGS result documents would crash
- NCBI: Fixed a bug where Sequence Search would crash when run on certain 3D structure documents
- MIRA Assembler: Fixed out of memory error caused by excessive information messages from MIRA going into the assembly report
- Primer design: Fixed a hang in the results dialog that could happen when Map Primers was run on a large sequence list, improved the dialog's usefulness
- Nexus export: increased speed when exporting large alignments as interleaved Nexus
- GenBank flat export: fixed issue with identifier that ends exactly at linebreak
- BLAST: default URL changed
Geneious Server:
- Patch a bug in Tomcat 6 introduced by a security update from Red Hat that breaks Geneious Server
Patch 7.1.6 (15 July 2014)
- Sequence View: Fixed hang sometimes when saving changes
- Contig View: Fixed poor performance on high coverage contigs when consensus numbering is on
- Map to Reference: Fixed selected sequence lists not showing up as available reference sequences in some situations
- Variant Finder: In regions of overlapping CDS annotations, fixed some variants not being found on the 2nd CDS annotation in some situations where an adjacent variant is also present.
- SAM/BAM import: Fixed crash importing files where the reference sequence name in the SAM/BAM file includes the '.fasta' extension
- SAM/BAM import: Fixed crash sometimes importing files when selecting only one of the potential reference sequences and importing to blank sequences for the others.
- SAM/BAM export: Fixed crash and/or failure to export when exporting multiple contigs
- Fixed a bug where users would get a crash on startup trying to load windows native libraries. Previously thought to be fixed, but wasn't.
- GenBank Exporter: fixed an issue where importing and reexporting a file to GenBank flat and xml format would lose some of the Geneious-specific information associated with the annotations.
- GenBank Exporter: updated the list of qualifiers and feature types, which was out of date.
- Export: Fixed non-ascii characters (e.g. Greek characters) not appearing correctly in exported files on Windows
- Export Graphs: Transposed csv so that each row (instead of column) represents a single position in the sequence or alignment (this means large files can now be imported into Excel)
- Annotate from database: Fixed bug causing only the best result for near-duplicates to be annotated sometimes instead of annotating all matching locations
- Annotate from database: Removed near-duplicates being annotated over the same region as a better match
- Annotate from database: Displays the range of similarity scores instead of just the best one contributing to an annotation that is obtained from multiple sources
- Transfer annotations: Fixed calculated similarity scores being lower than they should have been
- Fixed an issue with the Vector NTI importer failing to link some parent descendent documents
Patch 7.1.7 (22 July 2014)
- Fix a bug introduced in 7.1.6 where the GenBank exporter would crash on documents with polymorphism annotations
Patch 7.1.8 (17 Feb 2015)
- GFF import: Fixed incorrect codon start on reverse directed multiple interval CDS annotations
- Alignment View: When editing gaps or residues in a sequence with an annotation track, the position of annotations in the track in the referenced sequence are now correct
- Find Motif & Dotplot: Fixed bug causing these to occasionally fail to run
- Sequence View: GC% being lower than it should be due to gaps and ambiguities being counted as non-GC characters
- Blast Hits: corrected representation of transferred annotations in alignment and query centric view
- NCBI: adjusted to an XML change in the Gene db so that Organism is recognized correctly
- NCBI: Fixed a crash many users were experiencing on certain Gene summary documents
- Primer design: Prevented the user from selecting a certain combination of Salt Concentration options that was invalid and would crash primer3.
- Shared Database: Can optionally edit documents from future versions of Geneious even when it might cause data loss due to the future version having new data properties that this version can't understand.
Geneious Server:
- Fix server side custom BLAST database deleted during server restart under some circumstances
Patch 7.1.9 (26 May 2015)
- NCBI Gene Database: Implemented changes to new XML display format for E-Utilities/ESummary
Version 7.0 (3 September 2013)
Patch Versions:
7.0.1
7.0.2
7.0.3
7.0.4
7.0.5
7.0.6
- Copy with Annotations - annotations are now maintained when copying sequences
- Gibson Assembly - One-step cloning of fragments using Gibson assembly including automated primer design and batch cloning/shuffling
- Codon Optimization - Find rare codons or produce a fully optimized sequence based on a target organism and remove unwanted restriction sites at the same time.
- TOPO Cloning - One-step cloning of fragments into a vector using TOPO
- Workflows (Beta) - New interactive tool for creating automated workflows that run any of the existing tools in Geneious
- Alignment Features:
- Display nucleotide alignment as its protein translation (Option to hide nucleotides in Alignment View)
- Added 'Pairwise % Positive' on which indicates the percentage of amino acid pairs that have positive scores in the BLOSUM62 matrix.
- Improved quality of 'automatically determine direction' setting
- Sort sequences by the number of differences from the reference sequence
- Hold down the SHIFT key when inserting to push the alignment sequence left instead of right.
- Sequencing and Assembly Features:
- Coverage graph: Added visualization of minimum/mean/maximum coverage when zoomed out. Added highlight coverage above threshold option.
- Separate by Barcode: Included 454 Rapid MID barcodes, support for trimming barcode specific sequences from the other end, and better handling of primers/linkers containing ambiguities
- Fields and notes from contigs are transferred to the consensus when extracted, via Sequence View extraction, Generate Consensus Sequence operation, and assembly.
- Alignment/Contig View: Consensus sequence displays translation using the reference sequence CDS annotations when translation by annotation is on and the consensus sequence has no annotation at that position
- Contig View: Improved performance viewing data with high coverage variance (e.g. rnaSeq data)
- Consensus: When coverage or quality is below a specified threshold you can choose to call either ?, N, Gap, or the reference sequence value
- All newly created contigs will have a mean coverage field in the document table. All newly created reference sequence contigs will have a '% of reference sequence covered' field
- Read Mapping: Improved results when mapping to genomes with repetitive regions
- Variant Finder: 'Don't find variations in annotation types' and 'Only find variations in annotation types' settings now work on consensus sequence annotations (useful on de novo assemblies)
- New Downloadable Plugins:
- RAxML - Randomized Axelerated Maximum Likelihood
- GARLI - Genetic Algorithm for Rapid Likelihood Inference
- FastTree - Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
- LastZ - BLAST-like alignment tool for the pairwise alignment of chromosome-sized nucleotide sequences
- Bowtie2 - Sequencing read aligner
- Velvet - De-novo assembler for very short reads
- Dynamic primer editing allows modification of primer annotations and calculates characteristics in real-time as changes are made
- Primers are now designed on the consensus of alignments and contigs
- Primer Trimming: If you select only one end to trim from, the trimmed region will extend towards that end instead of respecting the direction of the primer.
- Primer Trimming: Made the 10,000 sequences limit at which it doesn't annotate trimmed primers user configurable from Preferences->General->Advanced->Trimming.maxSequencesToKeepExtraAnnotations
- BP, LR and One Step Gateway operations merged into a single Gateway operation
- Custom ladders for Virtual Gel: You can now modify the ladders and add new ones
- Enzyme table now has a search box to find enzymes by name
- All source properties on GenBank sequences (eg. country, strain) are now available as columns in the document table
- The following graphs in the alignment, contig and Sequence View can be exported to CSV and WIG file formats: Coverage, Identify, Sequence Logo (entropy), GC Content, Hydrophobicity, PI, Protein Coding Prediction, and Amino Acid Charge
- Fasta exporter: Added option to exclude sequence descriptions and option to not replace spaces in the name with underscore characters.
- Nexus exporter: Added option to replace spaces in the name with underscore characters.
- Batch rename: Can now rename fields of aligned sequences (when the sequences are writable)
- More special characters are now allowed in Annotation names and Meta-data fields (eg. greek)
- Copy Annotations in selected region allows selection of multiple sequences again
- Extracting multiple intervals from chromatogram now keeps sequence as chromatogram if any intervals contain chromatogram values. Same with sequence with quality only.
- Redesigned Add 5' extension operation that allows adding several extension parts in one step
- Added ability to drag and drop URL into Geneious to import the document at that URL (may not work with Internet Explorer, use Chrome instead)
- Annotations table: Minimum, Maximum, and Length columns now use less than or greater than symbols for truncated annotations
- Sequence searches now appear in the default operation results directory, rather than under the search results service
- Reduced memory usage on local databases containing lots of documents
- Protein summary documents from NCBI searches are automatically converted to full documents
- Sequence View: Uses the "Genetic Code" property on documents and saves changes back to that property rather than using its own preferences. Also allows you to set a default genetic code.
- Sequence View: When an annotation is selected, you can press the left then right cursor keys to set the cursor position to the left hand side of the annotation. Or press the right then left cursor keys to set the position to the right hand side.
- When extracting annotations of a single interval from a single sequence, it is now possible to concatenate them
- Custom Blast: Fields on documents added to the database (e.g. organism) now appear on the results of custom blast searches.
- Custom and NCBI Blast: Added option to automatically download full sequences of hits or just the region surrounding the hit.
- Sequence View: Right click menu option to 'Copy Name and Bases' is now available on stand-alone sequences
- Sequence View: Bases that have been edited are now highlighted in bold
- Add/Edit Annotation in Sequence View allows you to delete custom annotation types from the dropdown
- Primer Choosing: Improved performance choosing primers when you have thousands of primers in your database
- Sequence View Printing: Added option to turn off shaded annotations when printing
- Plugin Development: Added support for 3rd party plugins to provide statistics in the sequence/alignment/Contig View
- Improved Shared Database performance. Indexing of documents is also now done in the background rather than immediately.
Other Notes:
- Geneious now bundled with Java 7 on Windows and Linux
- Collaboration is no longer bundled with Geneious, it is now a downloadable plugin
- Mac OS X 10.5 Leopard is no longer officially supported
- Smart Agents/Folders removed from Geneious. Other aspects of agents are unchanged.
- "Find Annotations" renamed to "Annotate From Database"
Bugs fixed:
- Copying/transferring annotations between sequences in alignments excludes the annotated translation property of source annotations
- Sequence View: Fixed 'annotate & predict' results (e.g. trimming) being incorrect if you make changes (e.g. sorting data) while the operation is running
- Sequence View: Annotation tooltips wrap long property values to the next line instead of truncating them
- Fix issue where the Att site annotator would mistake AttB sites at the end of a linear sequence for AttL sites
- Improved recognition and handling of unreliable network file systems when storing your Geneious data on them
- Annotation types are now properly case-insensitive, eg. "CDS" is the same as "cds"
- Fixed poor performance when viewing some circular contigs containing sequences with large internal gaps
- Fixed some cases where setting custom colors of annotations didn't work
- Stopped the Mac OS firewall continually prompting about Geneious in many cases - modifying the max memory setting in Geneious will still cause the issue
- Many other minor bug fixes
Patch 7.0.1 (24 September 2013)
- Sequence Search: NCBI BLAST database names in Geneious now reflect those on the NCBI website more closely
- Sequence Search: BLAST result folders now remember which column they are sorted by when switching between folders
- Sequence Search: Improved progress and results reporting for BLAST searches
- Sequence Search: Simplified options for whether to download matching region, extended regions or full sequences.
- Sequence Search: Fixed bug causing downloading sequences to get unselected
- Sequence Search: Results exported from 7.0 can now be imported into 6.0 and later
- Sequence Search: Fixed crash when running on sequences in a shared database
- Contig, Alignment and Sequence View: Fixed mouse cursor going invisible or being incorrect sometimes
- Contig, Alignment and Sequence View: Fixed annotation text inside annotations sometimes extending outside the annotations
- Contig, Alignment and Sequence View: Reverting editing annotations on alignments now keeps the alignment aligned if possible
- Contig, Alignment and Sequence View: Improved performance dealing with genomes fragmented into thousands of sequences (for example 10,000 or more sequences, where some sequences in the genome are longer than 100,000bp)
- Contig, Alignment and Sequence View: Contig, Alignment and Sequence View: Improved performance and nicer rendering of annotations
- Primers: Improved handling of gaps when designing on an alignment
- Primers: Fixed crash editing the primer annotation of an oligo sequence
- Primers: Improved progress reporting
- Workflows: Added sample workflow to reverse complement all selected sequences, sequence lists, or alignments
- Workflows: Fixed crash when running some workflows on alignments or chromatograms
- Workflows: Added sample custom code workflow to set the truncated status on annotations
- Workflows: Improved custom code editor including code completion, context sensitive javadoc and nicer compilation errors
- Import/Export: Fixed crash which could occur when exporting unsorted contigs with trimmed regions to BAM+BAI format
- Import/Export: Respect RGB values in BED files
- Cloning: Gateway Cloning now displays information about the reaction it will perform before proceeding
- Cloning: Gibson Assembly will no longer fail if a primer has multiple binding sites, instead a warning will be displayed in the report
- Annotation Editing: Fixed some annotation types (e.g. trimmed or overhang) not being recognized after being edited
- Extract Annotations: Improved performance
- Removed Pfam services and operations
- Separate by Barcode: Fixed sequences being incorrectly assigned to barcode groups in some situations when the linker sequence isn't found. This happens when using linker sequences with large numbers of Ts or As near the ends and with high mismatches in the linker.
- Preserve annotations on consensus when concatenating alignments
- Sequence Search: Fix issue where downloaded full BLAST results did not replace their summaries
- Assembly: Fixed hang or poor performance viewing assembly reports which contain links to thousands of contig documents
- Variant Finder: Better default settings and improved strand-bias filtering on Illumina paired read data
- Fix a crash caused when using generate consensus on documents with inconsistent document fields produced by the Biocode LIMS plugin
- Alignment: Better results when using automatically determining direction on free end gap alignments
- Annotate From Database: It now will transfer truncated annotations from the source sequences
- Transfer Annotations: Similarity slider can be set to 0% to transfer all annotations in alignments regardless of similarity
- Fixed situation where floating license would have to be re-activated every time Geneious is started on some Macs
Patch 7.0.2 (8 October 2013)
- Contig View: Fixed crash sometimes when turning on 'Vertically Compress Contig'
- Contig View: Added option to sort by read direction
- Sequence View: Fixed names of sequences being incorrectly truncated sometimes
- Sequence View: Can use annotation properties of annotations in tracks as the displayed label for that annotation type
- Sequence View: Fixed setting sequences to circular on some sequence lists not working.
- Sequence View: Fixed poor performance and results being skipped sometimes when pressing enter to jump through filter matches
- Sequence View: Removed some unused annotation types from the annotation type drop down list and increased the scrollable region height
- Sequence View: Fixed crash occasionally when editing primers
- SamTools Variant Finder (Geneious Server): Fixed it not working when run from Contig View's 'Annotate & Predict' menu
- Assembly: The default assembly name now contains variables for the reads and reference sequences so you can set your preferred naming style once instead of on every assembly
- Assembly: Fix bugs when just saving 'used reads' without the contigs. The assembly report would say that no reads were mapped and the iterative mapper would only apply a single iteration
- Alignment: Fixed crash when trying to align two alignments together
- Workflows: Added option for creating branches in workflows
- Workflows: More comprehensive documentation for creating and editing workflows. And more examples
- Workflows: Added option to filter by document type
- Workflows: Primer design and testing can now be configured from workflows
- Workflows: Fixed 'Combine with earlier documents' using incorrect data set when referring to an earlier 'save & continue' step.
- Annotate from Database: Fixed crash when source sequences have undirected annotations on them
- ACE Importer: Fixed a bug where it would crash on some invalid ACE files
- General: Fixed hang or crash sometimes when moving, deleting or modifying lots of documents
- Primer testing: Fixed it not finding results in some cases on circular sequences with a target region
- Primer design: Option profiles no longer overwrite the target and included region when loaded
- NCBI BLAST: Fixed a bug where Binning searches would fail to bin all queries in a batch
Geneious Server:
- BioPerl no longer installed as part of Geneious Server as Velvet plugin is now self-contained
- Single machine install option configures Sun Grid Engine to use Classic spooling instead of BerkeleyDB for better stability
- Better error messages on both client and server when login failure is caused by an exception on Geneious Server
Patch 7.0.3 (16 October 2013)
- Fixed crash on startup for people who had used the beta
- Fixed crash when viewing 3D structures
- Copy/Paste of a single sequence region within an alignment preserves gaps
- Fixed drag and drop URLs not working on some systems.
- Fixed crash while indexing large tree documents when there isn't enough free memory
- Restriction Analysis: Fixed a bug where Find Restriction Sites wouldn't find some enzymes on a selection across the origin of a circular sequence
- Sequence Search: Fixed crash when modifying the query sequence
- Primer Testing: Fixed newly created primers sometimes not showing up in the available primers for testing
- Tree View: Labels set to 2 significant figures will display for example as 33 rather than 3.3 * 10^1
Patch 7.0.4 (30 October 2013)
- Import/Export: Fixed crash when drag and dropping attachments from Thunderbird into Geneious
- Import/Export on Linux: Fixed file selection problems in Import and Export file chooser dialog in Linux which could cause exporting to write to the wrong file
- Sequence Search: Fixed bug where searches on certain sequence lists weren't ignoring trim annotations.
- Alignment View: Fixed trees becoming corrupt when extracting sequences from a tree in the alignment view
- Tree Documents: Fixed some tree documents crashing when attempting to view or index them
- Linux: Fixed crash on some Linux systems (probably those with Synergy installed) whenever a sequence is viewed
- Sequence View: Fixed crash when converting some annotations into primer annotations
Geneious Server:
- Admin console not allowing certain special characters in entry of new user passwords
- Removed bottleneck in upgrade script that appears to hang when shared database uses large amount of disk space
Patch 7.0.5 (25 November 2013)
- Sequence View: Turned off the new 7.0 feature where edited bases are bold and the red squiggle for deleted bases because it was annoying in some situations. It can now be enabled from the editing annotation type popup menu.
- Sequence View: Fixed crash sometimes when open a document in a new window
- Sequence View: Fixed crash when choosing to edit all annotations of a particular type when there is only one annotation of that type
- Generate Consensus Sequence Operation: Stopped it wrongly using 'Highest Quality' on protein alignments
- Download Annotation Tracks: Fixed crash downloading some tracks, and fixed empty additional tracks which sometimes appear
- Fixed poor startup performance when 'Deleted Items' contains lots of documents
- Custom BLAST: Fix memory leak of open file handles which could cause Geneious to crash during or after using custom BLAST
- Chromatograms: Fixed crash in some situations when extracting or sequence searching from them
- Backup: Fixed problems when out of disk space during backup
- Backup: Made backup write directly to the backup drive instead of a temp file on the Geneious data drive first
- Sequence Search: Fixed crash after deleting sequences from a sequence list which was previously used as input to a sequence search
- SAM/BAM import: Fixed reads being paired with the wrong mate when importing some files
- Extract Annotations: Fixed crash in some cases when extracting entire sequences from alignments
- 3-D structure view: Fixed selection being offset from correct selection on some rare types of documents
- Import/Export on Linux: Fixed file selection problem in Import and Export file chooser dialog in Linux that could cause display error or a crash
- Batch rename: fixed a bug where types of documents with a custom field named "name" wouldn't be able to be renamed
- Primer design: fixed a bug where designing primers with certain target region/included region combinations on alignments would fail
- Primer design: clarified the expected format of the a custom mispriming library file
- Primer design: fixed bug where designed primers were being thrown away prematurely based on degeneracy
- Sequence Search/NCBI/Transfer annotations: fixed an issue in rare cases on translation searches where a "original sequences were modified" message would pop up. Transfer annotations would also fail.
- NCBI: Fixed a bug where some full sequences from certain protein summary documents would not download
Geneious Server:
- No longer require the home directory of the Geneious Server HOSTNAME linux account to be /home/HOSTNAME
Patch 7.0.6 (17 December 2013)
- NCBI Blast: Translation searches no longer incorrectly allow you to transfer annotations to query (which would result in wrong annotations)
- Geneious format import: Fixed crash when importing some types of documents from future versions of Geneious
- Alignment View: Fixed crash when extracting the consensus sequence along with other sequences from an alignment that has a tree attached to it
- Blast Text Format Exporter: Fixed a bug where it wouldn't export when there were changes made to a referenced query document
- Sequence View translation: When extracting a translation, fixed incorrect warning about the sequence not being a multiple of 3 sometimes
- Linux: Fixed crash on startup on some Linux systems
- Primer Editing: Fixed a bug where editing a primer in a pair on certain documents would crash
- Tree View: Fixed a bug where consensus values could be shifted to the wrong node when re-rooting a tree
- Assembly: Fixed poor performance when viewing one contig out of thousands produced by an assembly.
- Cloning: Fixed a bug where gateway would crash if one of the inputs had malformed annotations on it.
- Custom Blast: Fixed that manual setup steps for BLAST+ did not leave Custom BLAST fully set up
- BLAST: Fixed bug where translation searches would have incorrect Query Coverage field values
Geneious Server:
- New option to allow Geneious Server login only to members of a specified linux group
Version 6.1 (7 February 2013)
Patch Versions:
6.1.1
6.1.2
6.1.3
6.1.4
6.1.5
6.1.6
6.1.7
6.1.8
- Primer Design
- New cloning primer design task added for designing primers with fixed 5' binding positions
- Repeat library mispriming added to avoid binding to known repeats
- Primer extensions can now be chosen from the primer design options
- Designed primers now have nicer names
- Sequence View
- When adding or editing annotations you can choose which track they are on.
- Replaced the "Move all of annotation type" option with a more general "Edit all of annotation type" option.
- Added right click option to copy a sequence name or other displayed field.
- Removed restriction on maximum length of text that can be searched for as long as interpreting ambiguities is turned off
- Alignment/Contig View
- Added option to hide columns with more than X% gaps
- Can drag select the alignment numbering to select all sequences in alignments/contigs
- Added find dialog option to allow gaps between characters being searched for
- Improved rendering performance (5 times faster in some cases)
- Custom BLAST now supports BLAST+ (existing users will have to upgrade blast manually, new users get BLAST+ by default).
- Back Translate now has codon usage tables for producing unambiguous nucleotide sequence (uses EMBOSS tool backtranseq)
- DNA/RNA fold view now available on two sequences, showing how the two molecules bind to each other (uses Vienna rnacofold 2.0.7)
- DNA/RNA fold view updated with new stats panel, better probability color scheme and new energy models
- High/Low Coverage Finder: Added option to merge annotations less than a specified number of bases apart.
- More things are multi-threaded which makes them faster (e.g. trimming, read mapper indexing)
- De Novo Assembly: Slightly better results on gappy data
- Lengths Graph: Added option to display contig lengths
- New "Grade" column for sequence search results that combines E-value, identity and query coverage in to a single percentage
- Cut positions in enzyme table viewer split into count and positions for easier sorting
- Lambda PFG, Low range PFG and Lambda DNA-BstEII ladders added to virtual gel view
- New geneious.properties file can be used by admins to configure geneious
- Text View now available when several documents are selected
- New Bowtie2 assembly option added on Geneious Server
Bugs fixed:
- Circular contigs now correctly render graphs (e.g. chromatograms) on sequences that wrap past the circular origin
- Fixed a crash when importing primers from csv of longer than 36bp
Additional Notes:
- Sample documents have been changed significantly
- The Solaris operating system is no longer supported officially
- Most text is now rendered clearly on Retina display macs
- Trial licenses now have to be requested and activated
- Vienna rnafold updated to 2.0.7
- All EMBOSS tools updated to 6.5.7
- Bowtie updated to 0.12.8 (Geneious Server)
- SOAP2 updated to 2.21 (Geneious Server)
Patch 6.1.1 (27 February 2013)
New features:
- Sequence View: Can revert editing annotations (Insertions, Replacements, Deletions)
Bugs fixed:
- Alignment View: Fixed crash when searching for long text on alignments with the 'Allow extra gaps in sequence' setting on
- Alignment View: Fixed crash when clicking on annotations in pairwise alignments when the consensus sequence is off
- Contig View: Fixed it incorrectly scrolling down when zooming in sometimes
- Contig/Alignment View: Fixed hangs when deleting large selections. Also improved deletion behaviour to replace non-gaps with gaps when deleting
- Stop crash when starting up when data is stored on an unmounted network drive
- Fix issue where queueing for already-queued FlexNet license would stop you from getting the license when it came available
- Fix potential hang on shutdown (due to preference clearing issue)
- Stop sequences imported from VNTI's .gb format having "(modified)" appended to the name
- NCBI BLAST available in restricted version again
- Fix crash in feature finder when searching for features annotated on reverse of protein sequence
- Improvements to queueing behaviour of FlexNet and Sassafras floating licenses
- Nexus importer now importing attributes as document fields
- Fix crash in BAM exporter when multiple documents have same name
- Fix off-by-one error in Gateway annotator which could lead to crashes in Gateway operations
- Clipboard Csv/Tsv import now offers you the choice of which of the two formats to import as. Previously it would erroneously choose the first format which was well-formed.
- Fixed a bug where too many excluded regions were being sent to primer3 when primer design was run on some alignments
- Made several consistency changes when importing/creating primers that were too short or too long for primer3, across several tools
- Fixed a crash in Primer testing when a match on a circular sequence with mismatches fell over the origin
Additional Notes:
- BWA updated to 0.6.2 (Geneious Server)
- Velvet updated to 1.2.08 and Velvet optimizer updated to 2.2.5 (Geneious Server)
Patch 6.1.2 (4 March 2013)
Bugs fixed:
- Fixed Primer design with existing crash when existing primer doesn't match target sequence perfectly
- Removed ability to make shortcuts to system operations
- Fixed bug in PopSet full document download affecting number of results
- Fix issue with Gateway operations where the AttX1 site straddled the origin
- Fix issue with Sassafras licenses not releasing properly when released through Pro menu
Geneious Server:
- Streamlined Geneious Server installation procedure
- Under the hood changes to harden security in admin console
Patch 6.1.3 (25 March 2013)
Bugs fixed:
- Contig View: Fixed poor performance viewing large contigs with many hidden columns of gaps
- Contig View: Fixed reordering of sequences getting lost when saving on some contigs
- Contig View: Fixed incorrect translation on reads in circular contigs that wrap past the origin
- Sequence View: Fixed missing position labels at the ends of selected annotations sometimes and fixed incorrect position labels when resizing annotations
- Sequence View: Fixed paired reads being paired incorrectly after deleting sequences
- Sequence/Contig View: Fixed hang when deleting lots of sequences
- Sequence/Contig View: Fixed crash sometimes when deleting trim annotations
- Sequence/Contig View: Fixed crash and/or incorrect results when annotating or trimming multiple sequence lists after first sorting the sequences inside them
- Fixed a bug where Sequence Searches that were running at the time of upgrading to 6.1.0 would crash on startup
- Annotations Table: Fixed incorrect length of annotations crossing the origin of circular sequences
- Fix crash importing Nexus documents
- Fix unresponsiveness when running Modeltest from the PAUP* plugin
- Fix a crash that could occur when custom BLAST gives back results in unusual format
- Fix rare crash in Feature Finder
- Read Mapper: Fixed crash in rare situations when using iterative mapping
- De novo assembly: Fixed poor results in some cases when de novo assembling 454/Ion Torrent data
- Stop Geneious automatically checking Sassafras license out again when it is manually released
- Fix issue with BLAST+ only reporting 100 hits when searching for more than this
- Fix hang shutting down Geneious when there is blocked multicast socket
Patch 6.1.4 (9 April 2013)
Bugs fixed:
- Reference Assembly: Fixed incorrect handling of RNA data
- Reference Assembly: Fixed mapping results being offset from where they should be sometimes
- Coverage Graph: Fixed it being slightly offset from where it should be when hiding columns of gaps
- DNA/RNA Fold View: Fixed crash on some pairs of sequences
- Variant Finder: Fixed crash in rare cases when calculating p-values
- De novo Assembly: Better results on data with homopolymer style error models (e.g. Ion Torrent or 454)
- Fix issue where quality ended up on the wrong bases when concatenating a mixture of quality and non-quality sequences
- Fix issue where it was not possible to use GreenButton and a FlexNet license server at the same time
Geneious Server:
- Fix issue with PAUP* not running on Geneious Server
Patch 6.1.5 (13 May 2013)
Bugs fixed:
- Sequence View: Fixed it incorrectly scrolling down sometimes when drag-selecting regions
- Sam importer: Fix issue with read positioning in reads with a soft clip overhanging the start of the reference
- Shared Database: Fixed primers in shared databases not showing up in primer testing options sometimes
- Variant Finder: Fixed incorrect amino acid effects for variants on left directed CDS annotations where only the first and third position in a codon have varied
- De Novo assembly: Fixed hang when running on documents in a shared database
- Read mapping: When mapping reads containing ambiguities with the option turned on to map them to all matching locations, it could sometimes map a read multiple times to the same location.
- Reverse complementing sequences containing variant annotations now correctly reverse complements appropriate properties of the variant annotation
- Set paired reads: Fixed default direction indicator image showing forward/forward instead of forward/reverse
- "Other arguments" option in custom BLAST now working for BLAST+
- Fixed various issues that could occur when Geneious or plugins installed on a path with non-ascii characters (eg diacritics)
- Fixed "Bin into 'Has hits' vs 'No hits' when using BLAST+
- Fixed incorrect chromatogram and identity graph rendering when using the 'Hide columns over x% gaps' setting.
Patch 6.1.6 (20 June 2013)
Bugs fixed:
- Fix incompatibility with recent Java security update on Mac OS X that prevented use of Geneious on that platform
- Annotations Table: "Min (original sequence)" and "Max (original sequence)" were off by 2 for sequences that are reversed from their original sequence
- Sequence View: Fixed hang sometimes when pasting text that contains tab characters into the annotation filter box
- Sequence View/Annotations Table: Fixed crash sometimes when selecting a document to view
- Added guards against renaming a tree to non-unique or empty names
- Fixed crash when doing a "bin into 'has hit' vs. 'no hit' in database" search on an alignment
- Fixed crash importing fasta files that have undisplayable characters in their description
- Fixed issue where collaboration thought all its summary documents were from an unknown plugin
- Fixed crash when performing operations on a Mauve document with a region selected
- Fixed crash that could occur when importing fasta file with unusual characters in the description
- Fix issue with Geneious not picking up the right license when multiple users are licensed on the same computer
- Fixed hang on startup sometimes when connecting to a server database containing primer sequences or agents
- Sequence View: Fixed crash using annotation filter on some sequences
- Save as Image: Removed 16 million pixel limit on saved image size
- Fix crash that could happen when downloading from NCBI structure (or root NCBI service)
- Bypass hangs in FlexNet licensing which could cause Geneious to never finish starting up
- Stop crash that could occur when modifying sequences upon which an alignment is currently being performed
- Stop spurious "invalid license" which could happen when an old license is in your system and you try to use a FlexNet license
- Fix frame when translating multiple annotations from Sequence View
Patch 6.1.7 (4 November 2013)
Bugs fixed:
- Fix problem storing/retrieving documents with multibyte unicode in metadata on Geneious Server shared database
- Agents: Fixed hang on shutdown or editing agents if you change the host name of a server database which contains agents
- Contig View: Fixed poor performance or hangs when selecting large regions after viewing the annotations table.
- Read Mapping: Fixed incorrect results and/or crashes in rare cases when mapping reads with gappy error models to a circular reference sequence
- Read Mapping: Improved results when mapping to genomes with repetitive regions
- Shared Database: Fixed frequent failure to purge unused file data when using PostgreSQL 9
- Separate by Barcode: Fixed sequences being incorrectly assigned to barcode groups in some situations when the linker sequence isn't found. This happens when using linker sequences with large numbers of Ts or As near the ends and with high mismatches in the linker.
- Fix issue where the Att site annotator would mistake AttB sites at the end of a linear sequence for AttL sites
- Stopped the Mac OS firewall continually prompting about Geneious in many cases - modifying the max memory setting in Geneious will still cause the issue
- ACE Importer: Fixed a bug where it would crash on some invalid ACE files
- Consensus trim to reference sequence: Trims using gap character instead of ?
Geneious Server:
- Fix issue with unicode characters in names of files used as source data for documents in shared data base
Patch 6.1.8 (14 April 2014)
Bugs fixed:
- Import: Fixed crash when importing some types of documents from future versions of Geneious
- Custom BLAST: Fix memory leak of open file handles which could cause Geneious to crash during or after using custom BLAST
- Variant Finder: If find variants is run when there were unsaved changes on a small contig with paired reads, variants near the ends of the contig were wrongly filtered out due to strand bias
- SAM/BAM import: Fixed reads being paired with the wrong mate when importing some files
- UniProt: Fixed failure to search UniProt databases due to change on UniProt servers
- Alignment View: Fixed crash when copying annotations in tracks to other sequences
Version 6.0 (4 October 2012)
- Primer Design and Testing
- primer3 upgraded to version 2.3.4
- Hairpin and dimer characteristics now calculated as melting point (Tm)
- Design on sub-region of a long sequence is much faster
- Updated melting point calculation parameters
- Primer testing performance improved
- Selecting two nested regions (by holding ctrl/cmd) in the sequence view will now set the included and target regions
- Sequence/Alignment/Contig View:
- Reference sequence floats at the top like the consensus sequence
- Can choose to number just the alignment without also numbering the reference sequence
- Annotations with db_xref links and from dbSNP are now hyperlinked to relevant web site entry
- Statistics display the percentage of bases that are at least quality 20, 30 and 40.
- Added option to change the thickness of annotations
- Nicer positioning of annotation labels
- Can edit properties (e.g. description) of sequences in sequence lists and alignments
- Improved support for read mapping when choosing to map reads to multiple locations:
- Coverage graph and find high/low coverage weight reads less based on the number of locations they map to
- Variant finder and consensus sequence generator: Added option to ignore reads mapped to multiple locations
- Reference assembler supports using the "map reads to multiple locations" on paired reads
- Contig View: Added '# Mapped Locations' color scheme
- Contig View: Status bar indicates number of locations the read is mapped to.
- Assembler has new option to not map reads at all that would otherwise map to multiple locations
- Variants Finder:
- Added option to include the sequence names contributing to each variant in the annotation
- Added 'Homopolymer quality reduction' setting to assist in eliminating false variants
- Amino acid changes reported now take into account variants elsewhere in the codon
- Added 'Average Quality' property on annotations
- Extended option limiting variations to within annotations of a particular type to also allow finding variations within a specified range of those annotations
- Import/Export:
- Added VCF import
- Added support for publishing figures to SWF and EMF
- Added ability to import SAM/BAM file against subsequence of reference
- Fastq import can import multiple files with same quality settings
- Geneious can now import files that have been zipped or gzipped
- Assembly:
- De Novo Assembly: Added option to only use percentage of input data for better performance when you have too much data
- De Novo Assembly: Improved assembly results
- Reference Assembly: New fine tuning algorithm that generates much better results, is faster, and generally uses less memory
- Extraction:
- Extraction, reverse complement and translate have document history
- Fixed issue where extension ended up at wrong end of primer extracted from reverse strand
- Added 'Complement Only' and 'Reverse Only' operations (this is not in default distributions - it needs to be installed from the plugins window)
- Extract Annotations now lets you choose what other annotations from sequences are included in extraction
- New Feature Finder automatically annotates plasmids and other sequences with database of features
- Annotations Table in separate tab now supports editing
- Sequence/Alignment/Annotations Views: Filter box now provides more powerful field-based filtering
- Forwards compatibility. Geneious 6 will be able to handle most documents that people export or put in shared databases using future versions.
- Circular reference sequence assemblies: Contig View displays them correctly and consensus calling, variant finding and high/low coverage finding and statistics correctly handle them
- High/Low Coverage Finder: Nicer track names for contigs with reference sequences (like the variant finder has)
- Consensus: When the reference sequence has no coverage, you can now choose to call either ?, N, Gap, or the reference sequence value
- Find Duplicates operation gives option to create new sequence list containing duplicates
- Modified date field is no longer updated on documents used as input to operations
- GenBank "contig" download downloads the full document and not the documents that comprise it
- Sequence Search: Now automatically ignores leading and trailing trim regions
- Full screen now supported on Mac OS X Lion and above
- Improvements to transcription factor search output: Transcription factor name, clickable link out to Tranfac entry, explanation of quality values.
- New "Info" view tab which contains Lineage, History and Properties. Properties combines the previous "Notes" view with the ability to edit common fields like Description and Organism
- Shared Database: Folders that a user cannot view are now hidden by default. They can be shown again by right clicking on the root database folder.
- Tree View now shows consensus support just above nodes
- Profile Alignment plugin turned off by default
- Collaboration menu moved under Tools menu
- Lots of other little improvements
Bugs fixed:
- Sequence View: When zoomed out, adjacent annotations looked like they were overlapping
- Editing 'Topology' field directly instead of changing it via the Sequence menu didn't work
Additional Notes:
- Geneious is signed on Windows and MacOS. This means it can be downloaded from Internet Explorer 9+ without warning and Gatekeeper will not reject it.
- Geneious now requires Java 6. Geneious will no longer run on Java 5. This means Geneious will no longer run on
platforms where Java 6 is unavailable such as Power PC Macs and Mac OS X 10.4 (Tiger)
- Geneious is now only available in one package for Mac OS X. This runs in 64 bit mode by default, but can be
changed to run in 32 bit mode.
- Server Databases has been renamed to Shared Databases to avoid confusion with Geneious Server
- Changes to licensing:
- Geneious Pro/Basic terminology removed
- Must now enter a license or start trial when starting Geneious for the first time
- Geneious Pro days no longer occur
- Geneious now collects anonymous usage information (with your permission) to help us make improvements
Patch 6.0.1 (18 October 2012)
- Read Mapper: Faster and produces better results
Bugs fixed:
- Fixed an issue that could cause Geneious to crash frequently on Linux.
- Improved performance of initial document counting in the shared database
- Fixed issue with unformatted sequences being misidentified when starting with ID, FT or SQ
- Fixed crash when trying to add enzymes to list but no enzyme sets in database or inbuilt set
- Fixed crash translating regions from contigs of paired reads
- Improved consensus calling around homopolymer regions in 454 or Ion Torrent data
- Improved behaviour of SAM/BAM files on reads ending before or starting after the area covered by the reference sequence
- Made tracks delete when the last annotation on them is deleted (where that was not already the case)
- Fixed Shared Database compatibility with PostgreSQL 9.
- Primer Design and Testing
- Better explanations when primer design or testing is unsuccessful
- Testing now finds primers that bind across the origin of a circular sequence
- Primer design on alignments now handles gaps more correctly
- Target region is now respected when designing one primer direction
Patch 6.0.2 (1 November 2012)
- Added fastq export option to export paired reads to parallel files
Bugs fixed:
- Read mapping: Fixed incorrect read mapping results and/or poor performance sometimes with circular reference sequences
- 3D Structure View: Fixed a bug where the selection in the tree was being calculated incorrectly, causing the tree and selections to behave incorrectly
- Fixed bug where extraction of multi-interval annotations from long sequences with many annotations could result in extra annotations
- Made PMID show up correctly on PubMed documents
- Fixed extraction of primers from regions of alignments containing gaps
- Fixed crash when concatenating sequence lists or alignments such that that total number of bases was greater than around 2,000,000,000
- Fixed issue where Tree View options didn't update when saving document
- Fixed issue where jmol viewer selection misbehaved when a PDB document contains HETATM records prior to the last ATOM record
- Fixed a bug where primer design on alignments would sometimes return primers that were outside the specified product range for some of the aligned sequences
- Fixed a bug where primer testing would annotate matching probes as primers
- Batch rename: fixed a bug where the count and dup keywords weren't working when the new name only consisted of the keyword
- Fixed a bug where test with saved primers would occasionally crash with very old primer documents
- Fixed a bug where primer design would attempt and fail to run with product sizes smaller than the included region
- Added a warning when the user attempts to run an operation that determines primer characteristics, where [dntp] > [divalent salt]. This is currently not supported by primer3
- Fixed crash in the parent-descendant viewer
Patch 6.0.3 (6 November 2012)
- Corrected initial release date
Patch 6.0.4 (28 November 2012)
- Sequence View: Fixed hang working with annotation types in tracks that contain '_' or '.' in their type name
- Sequence View: Fixed crash in rare situations when clicking on annotations in contigs
- Sequence View: Fixed crash and/or loss of newly added annotations on consensus sometimes when saving contigs
- Sequence View: Fixed poor performance/hangs viewing large contigs with non-trim annotations on the reads
- Sequence View: Fixed statistics that are too small to read sometimes
- Reference assembly: Fixed crash and/or incorrect results when choosing to map paired reads to all matching locations.
- Reference assembly: Fixed poor sensitivity mapping to genomes of several hundred MB (larger genome sizes (e.g. human genomes) were fine). The increased sensitivity will also slightly improve small genome results.
- Reference assembly: Fixed poor sensitivity mapping reads spanning the origin of circular reference sequences
- Reference assembly/Find Annotations: Fixed crashes when running out of memory.
- Variant Finder: Fixed crash when there is an insertion variant in a repetitive region at the start of the reference sequence
- Contigs: Fixed crash when creating contigs with a single reference sequence exceeding 1.8GB
- Contigs: Fixed out of memory errors and poor performance when working with lots of contigs
- Contigs: Fixed crash when deleting the ends of circular contigs.
- Fixed crash when using consensus 'Ignore Gaps' setting combined with 'Assign Quality: Highest'
- Fixed crash in MUSCLE alignment when MUSCLE runs out of memory but still returns results
- Streamlined selection in 3D Structure View
- Fixed crashes when downloading Whole Genome Shotgun records from NCBI
- Fixed hangs associated with the use of the feature finder
- Fixed bug stopping Geneious from being able to change its max memory on Windows sometimes
- Fixed hang when extracting multiple large regions from a sequence list or contig
- Stopped errors from custom BLAST from being suppressed when the entire BLAST failed
- Fixed Gene documents having their dates one month in the future from where they should be
- Stopped Vector NTI database import from failing completely when a document's parents unexpectedly have length zero
- Fixed multiple dialogs being popped up when queued Sassafras license is checked out but user does not confirm
- Stopped NCBI Gene database downloading documents multiple times when there is a connection error with NCBI
- Added warning when large NCBI BLAST fails due to being too computationally intensive
- Fixed translation in all 6 frames from using frame one only
- Stopped stop codon from being included when extracting translation from Sequence View
Patch 6.0.5 (12 December 2012)
- Fixed crash sometimes when doing a COGS search
- Fixed a crash that would occur when downloading results of Geneious Server jobs after resuming
- Fixed crash sometimes when creating contigs or sequence lists. Most often when saving unused reads during assembly.
- Fixed crash sometimes when iteratively mapping pre-assembled contigs to a reference.
- Fixed annotations that should be hidden showing up when using 'Find Annotations' or 'Transfer Annotations' and crash when working with them.
- Fixed de novo assembly crash while analyzing reads
- Fixed a crash that would occur when batch renaming a mixture of documents with and without document fields (such as imported BAM files).
- Fixed sequences in alignments getting replaced with contents of other sequences when sequences were deleted or reordered in the sequence list the alignment was built from
- Stopped geneious reporting "hangs" when a dialog is shown for a long time as Geneious starts up
- Fixed crash when extracting duplicate regions from Sequence View
- Fixed crash downloading some Whole Genome Shotgun sequences from NCBI
- Improved progress when downloading some Whole Genome Shotgun sequences from NCBI
- Improved speed of downloading full NCBI Gene documents
- Stopped crash during import of SAM/BAM files with read groups of expected template length 0
- Improved calculation of expected template length when not given in SAM/BAM file
Patch 6.0.6 (13 February 2013)
- Fixed editing of multiple annotations adding properties present only on one annotation to all the other annotations
- Fixed crash and/or incorrect results in rare cases when mapping reads to a reference sequence with iterative fine tuning
- Fixed crash in rare cases when mapping reads to a circular reference sequence shorter than the read being mapped
- Fixed SAM import issues when some sequences not present, or when using "Use sequences in the selected folder
- Fixed deletion of BLAST databases
- Fixed crash when downloading some SNP results (including in searches of root NCBI folder)
- Fixed issue where BLAST could download wrong results when there were multiple hits against same database sequence
Version 5.6 (27 March 2012)
Parent-Descendant tracking:
- Sequences can be actively linked to each other as parent/descendants. Active links are created by all cloning related operations.
- When a parent sequence is edited, Geneious can propagate the changes to all actively linked child sequences, save the changes to a copy or deactivate the links.Pro-only
- Documents can also be inactively linked to each other which means there is a record of their relationship but changes cannot be propagated. All non-cloning operations create inactive links.
- New lineage view shows parent and descendant relationships, including active and inactive links and the operations that where performed.
Sequence View Improvements:
- Added 'By Direction' color scheme for coloring sequencing reads based on their direction
- Statistics show mean forward/reverse coverage of the selected region Pro-only
- Improved performance when viewing contigs with regions of very high coverage (e.g. 5,000+)
- Separated "Find in annotations" and "Find in Sequence Names" options to allow efficient annotation searching on big contigs
- Improved performance viewing big contigs with annotated reference sequences
- Can edit the color of individual annotations Pro-only
- Translation now displays both amino acids for ambiguous codons that translate to 2 possible amino acids
- Go to base now uses the un-gapped position for the reference sequence in assemblies
New annotation table:
- Allows bulk selection, deleting and editing of annotations Pro-only
- Improved performance on large data sets Pro-only
- Remembers column state between documents Pro-only
- Integrated with sequence view so it shares all the same controls Pro-only
Variation/SNP Finder Improvements:
- Added 'Minimum Strand-Bias P-value' setting for reducing false SNPs due to sequencing error Pro-only
- Better identification of tandem repeat amplification/reduction Pro-only
- Track names added to the reference sequence now include the sample name in the track name Pro-only
- Added "CDS Codon Number" field to indicate which codon in the CDS the SNP applies to Pro-only
- Added "CDS Position Within Codon" field to indicate which position within a codon (1, 2, or 3) in the CDS the SNP applies to Pro-only
Other New Features:
- New Align/Assemble menu replaces the separate Alignment and Assembly buttons to make it easy to choose the correct algorithm
- De Novo Assembly: Reduced memory usage, improved performance and more accurate memory usage estimates
- Improved performance importing fasta/fastq/sam/bam files
- Files that are copied from the desktop can now be pasted in to the document table or imported using Import - From Clipboard in the File menu.
- Primer Trimming: Improved performance (about 7 times faster) Pro-only
- Primer characteristics can now be used for reverse primers and primer pairs Pro-only
- Test with Saved Primers now records mismatch locations as annotations and in a new qualifier Pro-only
- Extract button added to Sequence Lengths Graph Pro-only
- Strip alignment columns can now strip columns containing a certain percentage of gaps Pro-only
- Enzymes view is now available when more than one sequence is selected Pro-only
- 2D DNA fold viwer added which is available on any nucleotide sequence under 3000bp in length Pro-only
- Distances view now has # Differences and # Identities matrices Pro-only
- Plugin Development/Public API: Improved documentation
- When generating consensus trees, they can now be saved to a separate document.
- Can sort documents by their color (new color column added)
- Shared Database: Improved performance
Bugs fixed:
- Reduced memory usage on long-lived databases by storing preferences more efficiently
Additional Notes:
- Existing Shared Databases require an updated schema that will make them incompatible with versions prior to 5.6.0.
Patch 5.6.1 (11 April 2012)
Features and Improvements:
- Improved fastq import quality format guessing and added dialog asking if the guess is correct if Geneious is unsure of the format
- Better track names when running variant finding
- Batch rename can now rename multiple selected sequence list documents and multiple selected alignments
Bugs fixed:
- Fixed hang using Sequence Logo graph on big alignments/contigs.
- Sequence View: Reduced memory usage when viewing lots (e.g. millions) of annotations
- Fixed occasional failure to copy documents or folders from a shared Database
- Fixed incorrect assembly results sometimes when mapping to a circular reference sequence
- Fixed a bug where Convert to Oligo was appending a duplicate number to the end of the Oligo's name
- Custom Blast Query-centric alignments no longer double up on annotations
- Fixed a bug that could cause primer documents in a shared Database to not be available in the primer chooser
- Marking a document read in a shared Database no longer completely re-indexes it
Patch 5.6.2 (23 April 2012)
Features
- Restored the old annotation table view
Bugs fixed:
- Fixed "There is already a track on this sequence with name..." error message when running various operations such as cloning and SAM import
- Fixed out of memory error when viewing some sequences
- Fixed a bug where the Csv importer wasn't importing Date fields correctly.
- Fixed an error that would occur when searching a shared Database using a number field
- Fixed an issue with Sassafras licenses not working
Patch 5.6.3 (15 May 2012)
Bugs fixed:
- Fixed crash importing or copying some documents into the "Searches" folder or sub-folder
- Fixed crash when viewing some circular sequences
- Fixed crash when saving some sequences from the Sequence View
- Fixed crash when importing some fasta files
- Fixed crash when mapping reads longer than the circular reference sequence
- Fixed crash when importing files from GenomeQuest
- Fixed annotation type drop down being filled with partial type names after entering a custom type
- Fixed hang when viewing big contigs with annotations on the consensus sequence
- Fixed hang when editing big contigs
- Fixed incompatibility with Microsoft SQL Server
- Fixed annotations going missing in some situations when adding annotations to an alignment/contig which references sequences in a sequence list
- Fixed 'compare annotations' not working correctly with multiple contigs selected
- Made changing restriction site annotations on a sequence not require deactivating active parent links or propagating changes to actively linked descendant documents
Patch 5.6.4 (13 June 2012)
Bugs fixed:
- Sequence View: Fixed the wrong region being selected by a mouse click when rendering is slow
- Sequence View: Fixed crash when clicking the mouse sometimes
- Sequence View: Fixed crash when running an 'Annotate & Predict' operation when "Show annotations" was off
- Sequence View: Fixed crash sometimes when saving tracks
- Sequence View: Fixed crash sometimes when viewing circular sequences
- Reference Assembly: Fixed annotations going missing from reference sequence when fine tuning big contigs
- Reference Assembly: Fixed reads being incorrectly aligned and/or assembler crashing when mapping gappy reads when some of them have trim annotations
- Tree View: Fixed crash when two sequences in a tree have the same name
- Annotation tracks are now preserved when running a BP Reaction
- Fixed potential hang on startup or shutdown when checking license
- Improved support for importing DNAstar, GenBank and GFF files
- Fixed crash in custom BLAST when binning sequences into hits and no hits
- Batch rename - now appends the correct parent document name when batch renaming sequences in multiple lists or alignments.
Patch 5.6.5 (26 July 2012)
Bugs fixed:
- Reference Assembly: Fixed crash or mis-assembly of reads mapped to circular sequences that are longer than the reference sequence
- Fasta Importer: Fixed an issue importing flat file with over Integer.MAX_VALUE characters
- BAM exporter: Improved the memory usage when exporting .bai
- Fixed an issue where Insert into Vector was creating the wrong number of intervals on a Multiple Cloning Site annotation.
- Fasta Importer: Improved issue where the importer naming sequences incorrectly when the option to rename identical sequences was on
- SAM importer: Fixed an issue where it was still giving wrong expected distance in some cases
- Fixed an issue where concurrent licenses were sometimes going missing on MacOS X Lion
- Primer Testing: Fixed a crash in characteristics for selection
- BAM importer: Improved memory/disk usage issues in using the Picard libraries
- Circular reference assembler: Fixed an issue when assembling reads more than twice the length of the circular reference
- Annotations table: Fixed 2 occasional crashes
- Shared Database: Fixed an issue where super-admin permissions weren't being realized
Patch 5.6.6 (15 October 2012)
Bugs fixed:
- Fixed issue where consensus tree builder was producing incorrect trees
- Fixed issue where reverse complementing consensus sequences would crash
- Fixed issue where SAM/BAM exporter was recording gapped lengths of sequences in the LN field
- Fixed issue where low complexity filter was ignored in BLASTs sometimes
- Fixed issues where BLAST results did not always include the best hits
- Fixed an issue where the Shared Database could become slower than expected on large MySQL databases
- Fixed an issue where primer documents stored in a Shared Database would show up multiple times
- Fixed ligate operation not respecting reordering of fragements when re-running due to changes in parent document
- Fixed issue introduced recently by NCBI where protein searches would sometimes crash
- Fixed issue where Geneious-style floating license was not always visible to all users once registered
Patch 5.6.7 (21 June 2013)
Bugs fixed:
- Fix incompatibility with recent Java security update on Mac OS X that prevented use of Geneious on that platform
Version 5.5 (30 August 2011)
Sequence View Improvements:
- New annotation track functionality that groups annotations from a common source so they can be rearranged, colored, shown/hidden, deleted etc Pro-only
- Added an interactive mini-map that shows your current position in the genome and a summary of annotations
- Added a real-time annotation filter in the annotation controls Pro-only
- Added a chromosome selector when viewing an entire genome as a sequence list (saves memory and improves performance)
- Added a slider for changing the zoom level on genomes
- Redesigned "go to position" to have a single input field and a shortcut button in zoom controls on genomes
- Annotations are arranged more efficiently on genomes
- Positions in big sequences are now rendered like 45.2 mb instead of 45,200,000
- Added ability to extract multiple primer annotations simultaneously
- Annotation generators can now run on more than one alignment simultaneously. Eg. "Find Variants/SNPs" Pro-only
- "Add Annotation" button can now create separate annotations for each selected region Pro-only
- Coverage graph: Added logarithmic scale option and added mean coverage indicator on scale bar.
- Can click on annotation types in the controls to change all annotations of that type to a new type Pro-only
- Added "Copy (reverse complement)" to right-click popup menu
Other new features:
- New One Step gateway operation that does BP and LR reactions in one step Pro-only
- New Download Annotation Tracks operation to annotate genomes with data from Broad Institute Pro-only
- New CSV/TSV Importer: Import primers, probes and nucleotide/amino-acid sequences from spreadsheets
- All operations can now have their setting saved to a profile for re-using later or sharing with other people Pro-only
- New Support button that makes it easier to contact our support team and attaches system information so we can answer you more efficiently
- New 'Compare Annotations' operation to compare annotations of different types on a sequence Pro-only
- Primer Testing: Can now test a selection of primers from your database Pro-only
- New graph view displaying distribution of paired read distances in a contig Pro-only
- Distances view now works on alignments and can display a percent identity matrix (plus other small improvements) Pro-only
- Share Geneious documents and visualizations with your friends and colleagues via Email, Twitter or Facebook
- New TSV (Tab separated values) exporter
- Import sequences by pasting straight in to Geneious
- New checkbox column in table makes it easier to select multiple documents (no key presses required)
- SAM/BAM importer
- Improved performance and progress reporting
- Groups unmapped sequences by reference when known
- Can import more than one SAM/BAM file at once
- Find Variations/SNPs improvements Pro-only
- Added option to specify what properties of CDS annotations to copy to SNP annotations. Added CDS interval number property to SNP annotations
- Added p-value to variations and added a maximum p-value threshold for finding variations. This fixes incorrect variations reported around 454 homopolymer regions
- Added option to find variations within the sample (rather than comparing to the reference sequence)
- Ambiguities characters are now interpreted instead of being treated as different character types
- Assembly improvements Pro-only
- Better results when assembling to large reference genomes
- Added setting to save used reads (and optionally their non-mapping mates)
- Increased maximum reference sequences from 10,000 to 25,000 and added Preferences->General->Advanced->Assembly.maxReferenceSequences to increase it further (although this is not recommended as performance will be poor)
- Added 'Map multiple best matches' setting (for unpaired reads only) to read mapping/reference sequence assembly
- Added 'Assemble each sequence list separately' setting for performing multiple assemblies in one step
- CSV export can now include complete sequence
- Chromatograph View: Highlights the selected region from the sequence view
- GFF importer imports GTF format
- GFF importer more memory-efficient
- Strip alignment columns: can now strip every third position or columns containing one or more gaps Pro-only
- Transfer annotations: Added option to transfer annotations to the consensus sequence Pro-only
- Annotations table: Minimum, Maximum and Length columns values no longer include gaps in calculation. Added new columns with the old values Pro-only
- Annotations table: Added horizontal scrollbar and auto-size width of columns Pro-only
- Annotations table: Enhanced performance and fixed hangs when sorting or filtering extremely large numbers of annotations Pro-only
- Set Paired Reads: Added option to pair reads by name and now handles missing reads Pro-only
- Concatenation can now add NNNNN spacers between sequences Pro-only
- New column on contigs and alignments that displays the reference sequence name
- GenBank Flat importer now copes if there's no locus
- Now possible to import CAF file(s) and other file(s) simultaneously
- FASTA exporter can limit lines to 80 characters
- ClustalW is now bundled with Geneious Pro-only
- Added ability to release floating license Pro-only
Bugs fixed:
- Fixed partial CDS annotations (which include only a subset of the full CDS intervals) displaying out of frame annotations when extracted from a document containing the complete CDS
- Fixed deletion annotation at end of sequence not being displayed in Sequence View
- Batch rename now offers Description of the sequences in an alignment as a readable field when renaming
- Primer characteristic calculation including during oligo import from VectorNTI much faster
- Fixed crashes when alignment engines like MUSCLE and ClustalW return no alignment or unexpectedly return a local alignment
- Reduced memory usage required to move large documents from one folder to another
- Sequence similarity statistics respect trim annotations better
- Improved speed of FASTA im/exporter
- Improved speed of Find Duplicates
- Decreases memory usage of "Extract sequences from list"
- Avoided hang when adding custom BLAST database which produces lots of errors from formatdb
- Stopped GenBank exporter adding name label to features in unmodified documents
- Fixed crash when extracting contig from contig and some sequences in the extract region consist entirely of gaps
- Made Gateway Cloning cope with sites over origin when sites are attX1 and attX2; better error message for multi-site
- Stopped dialog popping up repeatedly if support on your permanent license expires while Geneious is not running
- Geneious now deletes file results from cancelled backup
- Fixed crash in RNAFold when output in unexpected format
- Fixed crash in SAM importer when file contains unaligned records without base sequence
- Fixed crash in SAM importer when encountering the X operator
- Fixed crash in download from NCBI when mandatory element missing
- Stopped ClustalW importer potentially importer alignments with mixture of nucleotide and protein sequences
- Stopped Custom BLAST losing document fields such as organism
- Stopped VNTI import crash when different molecules have custom fields with different fields
- Improved performance when editing bases in a genome
- Stopped Geneious assembler falsely identify regions in large genome as repetitive (and not mapping reads there)
- Fixed an issue which caused adding of documents to a shared Database to be significantly slower in v5.4
Patch 5.5.1 (19 September 2011)
New features:
- Annotations table: Added new columns with the minimum and maximum values in original sequence coordinatesPro-only
- BLAST query and hit sequences have description Pro-only
Bugs fixed:
- Fixed a bug where Batch Rename would fail to rename large sequence lists.
- Greatly improved speed of back up operation when doing full archive backup (no longer uses compression)
- Fixed custom fields being lost when exporting documents in Geneious format and importing them on another machine
- Fixed so that if you unselect the document while an 'annotate & predict' operation is running you can still get the results
- Fixed some fields not getting indexed for searching on big documents
- Fixed out of memory errors when indexing big documents
- Bug fixes in Sequence/Contig View
- Fixed crashes and hangs caused when trying to view too many tracks to fit in memory
- Fixed tracks crashing or behaving wrongly after reordering sequences
- Fixed track names being rendered too close or overlapping with the sequence name
- Fixed crash when viewing sequence lists containing tracks after some sequences have been deleted from the list
- Fixed crash when saving some contigs after seeing a conflicting changes message
- Fixed 'Annotations are arranged more efficiently on genomes' not working on circular genomes
- Changed units in Sequence View from Mb to Mbp
- Fixed annotations in tracks on consensus sequence appearing in the wrong location when 'hide gaps in reference sequence' is on
- Bug fixes/improvements in UCSC annotation track downloads Pro-only
- Warning if chromosomes are wrong length
- Nice names for genomes
- Better sorting for genomes/chromosomes
- File size does not stop displaying when you change chromosomes
- Stop displaying tracks that cannot be accessed by HTTP
- Fix issue where annotations could appear on the wrong chromosomes
- Allow annotation of sequences regardless of what documents they're grouped into (eg 1 standalone sequence and 2 sequence lists)
- Fixed horrible performance when running UCSC again without having saved the changes produced from an earlier run
- Improved memory efficiency of BED importer so you can import a densely annotated genome (eg SNP files from UCSC) in a small amount of RAM
- Bug fixes/improvements in SAM/BAM im/exporter
- Fixed issue finding reference sequences when importing SAM/BAM files with no header
- Fixed crash when exporting sequence with unreasonably high quality to SAM/BAM format
- Fixed crash importing with a reference with quality that has gaps introduced
- Fixed behaviour when importing or exporting contigs where one or more reads start after the end of the reference
- Fixed crash when file consists entirely of pairs without their mate
- Bug fixes/improvements in extraction/reverse complementing/translating in Sequence View Pro-only
- Changed behaviour of extraction of whole sequences from alignment to create new sequences rather than going to existing references
- Fixed crash when extracting annotation with two identical intervals on same sequence
- Made options remember preferences on appending "extraction" to names, extracting to alignment vs sequence, extracting selected vs entire sequences
- If you extract a whole circular sequence from an alignment the result is now circular
- Fixed bug where Jmol view did not restore state first time showing molecule after save
- Fixed crash in ACE importer when bases are invalid
- Fixed GenBank importer not offering to create sequence list
- Fixed bug where Geneious thought you could run annotation generators on unaligned sequences when the Sequence View wasn't loaded
- Fixed assembly crash when assembling existing contigs containing trim annotations covering gapped regions
- Annotations table: annotations that start or end at the origin of a circular sequence now show min/max values of the sequence length rather than 0Pro-only
- Annotations table: now displays annotations from consensus sequence tracksPro-only
- Annotations table: now remembers widths of resized columnsPro-only
- Annotations table: sorts decimal and scientific format numbers correctlyPro-only
- Fixed issue where the extraction of an annotation with overlapping intervals would end up with extra intervals
- Made fasta and fastq importer replace preformance-killing names with better ones
Patch 5.5.2 (26 September 2011)
Bugs fixed:
- Sequence View: Fixed tracks and annotation types in tracks sometimes not respecting the on/off state of the checkbox in the controls.
- Sequence View: Fixed editing colors of annotation types in tracks not being persistent
- Sequence View: Annotation types within tracks and the mini-map are now alphabetically sorted instead of random
- Sequence View: Fixed the left/right annotation navigation arrows not being enabled when they should be
- Sequence View: Fixed bug when filtering annotations in tracks the mini-map wasn't updated to reflect the filter
- Sequence View: Fixed hang loading large sequence lists
- SNP finding: Fixed bug introduced in 5.5.1 where annotations would be offset from where they should be
- Assembly: Fixed trim annotations getting lost during assembly sometimes
- Improved error dialog when a bug in a document causes the search indexer to crash every time Geneious starts. It now tells you how to prevent it from happening in future
Patch 5.5.3 (10 October 2011)
Bugs fixed:
- Assembly: Fixed crash sometimes when generating assembly report
- Assembly: Fixed crash sometimes when assembling gappy reads to a circular reference sequence
- Assembly: Fixed 'Map multiple best matches' mapping reads with gaps to the same location multiple times
- Alignment/Contig View: Fixed 'Hide gaps in reference sequence' discarding annotations covering gapped regions in the reference sequence
- Alignment/Contig View: Fixed crash when saving changes made to some alignments
- Contig View: Fixed changes getting lost in some situations when saving after editing the reference sequence in a big contig
- Contig View: Fixed hang sometimes when selecting on big contig documents
- Sequence View: fixed crash pressing ctrl-alt-g (go to residue) after selecting a document but before the Sequence View has finished loading
- Sequence View: Fixed crash sometimes if there isn't enough memory to load a big track on a sequence
- Sequence View: Fixed annotations in tracks getting drawn on top of other sequences in some situations
- Sequence View: Fixed crash when editing some trimmed sequences
- Sequence View: Fixed very slow initialization on sequence lists containing thousands of sequences with tracks on each sequence
- Sequence View: Fixed undo not working correctly when dealing with some types of changes to tracks
- Sequence View: Enabled genome viewer chromosome selector (available when at least one sequence has 100,000 or more bases) on sequence lists with more than 1000 sequences
- Local Database: Fixed failure to save documents sometimes
- SNP finder: Running on multiple contigs at once that referenced the same reference sequence would generate identically named tracks and only the first one would get displayed
- Sequence View: Fix bad performamce extracting millions of reads from a sequence list
- Sequence View: Fix crash extracting sub-alignment containing sequences of all gaps and the consensus
- Fixed tracks not getting saved sometimes when saving them on contigs/alignments
- Fixed a few crashes in the SAM/BAM importer
Patch 5.5.4 (7 November 2011)
Bugs fixed:
- Sequence Search: Fixed crash sometimes when doing a sequence search
- Sequence View: Fixed crash after deleting sequences in genome lists
- Sequence View: Fixed hang/crash when resizing some trim annotations
- Sequence View: Fixed crash clicking 'go to next annotation' button on some restriction site annotations
- Sequence/Contig View: Fixed crash if you delete a track, create one with the same name, and click save
- Sequence/Contig View: Fixed crash when loading a document that previously had an annotation selected in a track, but that track was turned off while viewing another document
- Alignment/Contig View: Fixed not rendering SNP/coverage annotations on the reference sequence that lie past the ends of the reference sequence
- Alignment/Contig View: Fixed it saying you need to zoom in to view reads on contigs that only have a few reads
- Alignment/Contig View: Fixed occasional crash when dragging bases/gaps around during alignment editing
- Alignment/Contig View: Fixed out of memory crash sometimes when saving new tracks
- Alignment/Contig View: Fixed crash sometimes when removing chromatogram sequences from a contig
- Assembly: Fixed crash in some cases when mapping a contig to a circular reference sequence. And improved results so that contigs spanning the origin map individual reads to both sides of the origin
- SNP Finder: Fixed crash on some data sets.
- SNP Finder: Fixed it incorrectly reporting 'no protein effect' when there is a deletion or insertion that doesn't change the amino acid at that point
- SNP Finder: Fixed it not reporting results correctly when there are overlapping CDS annotations
- SNP Finder: Fixed it not reporting results when choosing to find in CDS annotations only with 'analyze effects on translation' off
- SNP Finder: Fixed p-value missing from results in some cases when using exact p-value calculations
- Set Paired Reads: Fixed crash when pairing multiple sequence lists by linker.
- Set Paired Reads: Fixed crash when repairing reads with mixed relative orientations.
- Annotations table: Fixed very slow sorting
- Annotations table: Fixed occasional crash when no longer viewed
- Primer Design: Fixed a bug where sequences designated as probes were showing up with a forward primer annotation instead
- Primer Design: Fixed a bug where the salt concentration was not being taken into account when calculating TM of primers
- Primer Design: Fixed a bug where calculating characteristics was failing on multiple selections
- Fixed crash sometimes when deleting a folder
- Search index: Fixed crash sometimes when building search index for contigs with tracks
- Made changes to NCBI BLAST to adhere closer to the guidelines given by NCBI. Geneious will not hit NCBI limits
as easily. Also removed the 11kbp sequence length constraint from BLAST searching.
- Ace exporter: fixed a bug where it was exporting gap qualities
- Fixed major crash under Java 7
- Fixed issue where Geneious reports incorrect codon_start on CDSs on documents downloaded from NCBI which have foreign intervals
Patch 5.5.5 (21 November 2011)
Bugs fixed:
- Alignment/Contig View: Fixed crash when saving tracks if a track with the same name is created on a referenced sequence from a different view
- Alignment/Contig View: Fixed crash when saving if you had selected an annotation and shift-clicked in another sequence before saving
- Variation/SNP Finder: Fixed crash when using the "Find Only SNPs" option
- Assembly: Fixed crash when using the 'Minimum overlap identity' setting with a circular reference sequence
- Shared Database: Fixed an issue that would create duplicate folders in the Sources tree.
- Shared Database: Fixed a security issue when using the Microsoft JDBC driver and making use of integrated
security rather than the one bundled with Geneious.
- Patched NCBI Genome service to mimic its old behaviour after NCBI released a new Genome database incompatible with Geneious
Patch 5.5.6 (5 December 2011)
Bugs fixed:
- Alignment: Fixed annotations not being reversed and lost references when alignment automatically determines directions
- Primer search: Display a message when search index is being rebuilt instead of just showing an empty table
- Worked around a memory leak bug introduced by MacOS Java 6u29 that was causing crashes and freezes after a recent system update from Apple
- Fix issue on Mac OS where the main window would minimize on startup then be unresponsive (also caused by Java update from Apple)
- Shared Database: Fixed excessive slowness when there are a large number of additional document XML keys in the database
- Shared Database: Fixed modification of database blocking retrievals until it completes
- GFF importer: Fixed crash when sequences in list are not editable
Patch 5.5.7 (12 March 2012)
Bugs fixed:
- Sam/Bam importer was using excessive memory and temporary files importing sam/bam files with lots of reference sequences
- Fix hang that could occur on shutdown
- Shared Database: Fixed incompatibility issues with Microsoft's JDBC driver for SQL Server that were introduced in 5.5.6
Patch 5.5.8 (30 April 2012)
Bugs fixed:
- Fixed random crashes revealed by spurious wakeup bug introduced in Java update from Apple
- Fixed crash in the dotplot revealed by bug in Java update from Apple
- Fixed error message in NCBI services due to large batch size requests
Patch 5.5.9 (21 June 2013)
Bugs fixed:
- Fix incompatibility with recent Java security update on Mac OS X that prevented use of Geneious on that platform
Version 5.4 (29 March 2011)
New features added in Pro version only:
- Support for Multi-site gateway cloning
- BAM format import and export (including BAM index file)
- BED format import and export
- SAM format export
- Set the color of folders and documents in local and shared Databases
- RNA Fold View scrolls to selection
- Better results when reference sequence assembling.
- Codon usage statistics added to the Statistics tab in the Sequence and Alignment view
- The direction of sequencing reads can be set before the assembly process using "Set Read Direction" in the Sequence menu
- Improved performance and greatly reduced memory usage when dealing with large numbers of sequences (both stand-alone and in contigs)
- BLAST searches now have the option to return a query-centric alignment document only
- BLAST searches now have the option to bin queries into those with hits and those with none, without the need to download entire hits (faster than a standard search)
New features:
- Added "Whole Words Only" checkbox to local documents searching so that you can search for partial words
- Added "Find All" button when using "Find in Document" on the sequence/Alignment View
- Can select multiple folders for moving/deleting and for showing the contents of them all at once
Bugs fixed:
- When a sequence is circularized, annotation intervals extending past the ends of the sequence are now truncated
- When a sequence is de-circularized, annotation intervals spanning the origin are split into multiple intervals
- Fixed poor performance when viewing some sequences with over 100,000 annotations
- Empty sub-folders are now kept when exporting folders
- Separate by barcode works on already paired reads and lets you choose which sequence in the pair has the barcode
- Fixed problem with garbled fonts on some systems
- Fixed de novo assembler running out of file handles on machines with lots of processors
- Greatly improved the speed at which Geneious performs large batch BLAST searches
- Fixed crash when loading some contigs (which would also cause search index to crash)
Patch 5.4.1 (19 April 2011)
New features:
- Added support for NCBI genetic codes 16, 21, 22 and 23
- Enabled Chromatogram view by default and improved user interface
- Made split view on a circular sequence not rotate the view when at minimum zoom when synchronizing the selection with another view
Bugs fixed:
- Fixed bug in Variant/SNP finder where positions with multiple variations from the reference sequence were incorrectly labeled as insertions.
- Fixed bug where searching for a sequence name or annotation or sub-sequence that start on the first base of a sequence were sometimes being incorrectly reported as not found
- Fixed some performance issues with large contigs
- Fixed GC graph frame plot offset by 1 base in some positions
- Fixed crash when trimming some sequences
- Fixed crash when reference assembling trimmed sequences
- Fixed crash creating editable copy of blast results
- Fixed paired reads becoming unpaired when editing a contig or sequence list
- If a sequence includes its genetic code (e.g. GenBank sequences usually do), the Sequence View now uses that as the default genetic code in the translation options
- Fixed translation giving incorrect first amino acid on some translations (e.g. for the standard genetic code, CTG should translate to M instead of L when it is the first codon)
- Adjusted NCBI Structure View to adapt to changes at NCBI's end
- Improved error messages in Gateway Cloning
- Fixed Geneious sometimes crashing (not caused by doing anything in particular)
- Fixed a bug that would cause a progress window to stick around when connecting shared Databases on start up
- Fixed crash that occurred when deleting documents while having multiple shared Database folders selected
- Fixed hang when viewing sequence lists containing long sequences
- Fixed Geneious crashing when running out of disk space
- Fixed crash when circularizing some sequences
- Fixed a crash that would sometimes occur when resuming a BLAST search
- Fixed a crash when clicking on consensus sequences annotations that extend outside the bounds of the alignment
- Fixed bug during large contig creation in 5.4.0 where contigs were prone to crashing later and had performance problems when viewing them
- Fixed bug causing large contigs or sequence lists to occasionally crash
- Added progress to pfam operations
- Fixed issues with some file import terminating early
- Stopped ability to export files with characters in them that were not legal in filenames
- Fixed crash when using GFF or BED importer to annotate certain sequences
- Added a trial
- Fixed odd behaviour in SAM/BAM exporter when document contains a mixture of paired and upaired reads
- Fixed crash in PopSet when downloading a document that has no date
- Stopped export of GenBank sequences using wrong XML type for Seq_other-seqids field
- Fixed concatenation of protein sequences
- Decreased memory usage when downloading long sequences from GenBank
- Made Newick importer more memory-efficient
- Fixed issue affecting Mafft alignments of RNA
- Fixed crash when extracting from an alignment where the reference sequence is not the first sequence
- Fixed bug where a reference sequence could be assigned to an extracted alignment even when there is none
- Fixed issues where extracted alignments could contain sequences consisting only of gaps
- Fixed slow performance viewing some contigs
- Fixed very slow performance (hang) when editing some big alignments/contigs
- Fixed crash when trying to import more than one SAM/BAM file at once
- Fixed hang when selecting similarity or by annotation color scheme on large contigs
- Annotation Table now displays trimmed regions on all sequence lists
- Annotation Table now displays annotations from both views of a blast hit
- Improved dotplot view initial loading time
- Fixed issue with reordering of sequences with overhangs not being respected during concatenation
Patch 5.4.2 (25 April 2011)
Bugs fixed:
- Reduced excessive memory usage by Nexus exporter
- Reduced excessive memory usage by fasta custom BLAST database adder
- Fixed crash when exporting sequence to SAM file with < 2 characters in name
- Improved performance of trimming
- Fixed crash creating Pfam documents using Pfam 24
- Fixed crash when trying to create an aligment of 1 sequence only
- Fixed crash deleting or changing reference sequence in big contigs
- Fixed incorrect amino acid and codon usage statistics after manually editing CDS annotations
- Fixed crash due to too many open files when dealing with large sets of contigs
- Fixed a crash in BLAST when running a search on PDB documents
Patch 5.4.3 (12 May 2011)
Bugs fixed:
- Fixed extra highlighting showing up when highlighting disagreements in the translation of a nucleotide alignment
- Fixed out of memory crash when selecting a big sequence list or contig while the fasta viewer plugin is enabled
- Fixed crash when importing sequences which contain invalid nucleotide or amino acid characters
- Fixed "fromKey>toKey" crash when importing SAM/BAM file
- Fixed crash importing SAM/BAM file when soft clipped region overhangs the start of the reference
- Fixed crash adding enzymes to set
- Improved trimming performance
- Improved SAM/BAM import performance when importing file with multiple references
- Modified Gateway to support use of destination vector with multiple attR pairs
- Fixed queuing misbehaving on a FlexNet floating license with multiple seats
- Fixed crash extracting from alignment where sequences have been deleted
- Fixed crash during re-assembly if the input contig which contains a reference sequence has sequences that don't overlap the reference sequence
- Fixed crash when extracting zero length annotation from annotations table
- Fixed .fq extension file not being recognized as fastq
- Fixed possible issues wih file handles when importing many small contigs from ACE or SAM/BAM files
Patch 5.4.4 (7 June 2011)
Bugs fixed:
- Sequence View: Fixed crash when attempting to display some documents
- Sequence View: Fixed crash when finding ORFs or restriction sites on some sequences that have trim annotations
- Find Variations/SNPs: When analyzing the effect on CDS, the amino acid/codon changes property could sometimes have additional incorrect codons appended to the correct amino acid/codon changes.
- Find Variations/SNPs: If you turned on "Find SNPs Only" for a contig with a reference sequence, next time you search for variations on a contig without a reference sequence, it would find no results
- Fixed an issue with batch rename failing on certain combinations of documents
- Fixed an issue where running sequence searches from old versions of Geneious would crash Geneious on startup
- Fixed crash when importing sequences which contain invalid nucleotide or amino acid characters
- Sequence View: Fixed crash when using 'Color by Annotation' color scheme
- Assembly: Fixed crash when assembling paired reads to a reference sequence on some data sets
- Fixed bug where Annotation Table would sometimes select a different annotation to the one selected in the Sequence View
- Annotation Table now displays the value of "Sequence" annotation qualifiers, rather than displaying the actual sequence the annotation covers
- Contig View: Fixed crash when saving after deleting all the bases from a sequence
- Fixed incorrect PCR product size given in primer annotation
- Fixed crash when exporting .qual format file without accompanying fasta file
- Fixed crash when creating or extracting from big protein alignments
- Fixed issues where 64-bit windows users cannot activate on 32-bit Windows
- Fixed fastq export producing corrupt files on consensus sequences
- Fixed an issue where Geneious had to be restarted in order to use Trim by Vector or COGS BLAST after set up
- Fixed 'Find in document' keeping every document you use it on in memory
Patch 5.4.5 (30 June 2011)
Bugs fixed:
- Fixed changes being lost when making changes to an alignment built from a sequence list
- Fixed occasional crash exporting in SAM/BAM format
- Fixed crash that can happen downloading full documents from a tblastn run
- Fixed bug that can cause sequences extracted from tree document to be in the wrong order
- Fixed crash that can occur importing ACE files with reads starting or ending with gaps and having trimmed regions
- Removed possibility of crash from removing invalid bases from sequences with quality/traces on import
Pro-only features now enabled in Geneious Basic:
- All import and export
- Visualisation including circular sequences, chromatograms, color schemes, translation, highlighting, dotplot etc
- Teaching tutorials
- Save as PDF and SVG
- NCBI Gene and SNP databases
- Alignment options
Patch 5.4.6 (25 July 2011)
Bugs fixed:
- Fixed crash when creating contigs more than 270 million gapped base pairs long
- Fixed some protein sequence lists converting to nucleotide sequence lists or crashing (likely to occur when sequence searching using bin into 'has hit' vs 'not hit')
- Fixed crash when removing trimmed regions from some sequence lists when the trim annotation was selected prior to trimming
- Fixed case sensitivity in Separate by Barcode
- Fixed a problem with the installer which was causing Geneious to crash after upgrading
- Query centric view is no longer Pro-only
- Fixed agents so they won't download the same documents multiple times
- Fixed a problem which was allowing corrupt BLAST agents to be created, crashing Geneious
- Fixed crash when editing a sequence list that had been used as a BLAST query
Patch 5.4.7 (21 June 2013)
Bugs fixed:
- Fix incompatibility with recent Java security update on Mac OS X that prevented use of Geneious on that platform
Version 5.3 (15 November 2010)
New features added in Pro version only:
- Next-Gen Sequencing:
- Can split unprocessed 454 paired reads apart based on the presence of a linker in the middle of a sequence using 'Set Paired Reads' from the Sequence menu
- Can split multiplexing data (e.g. 454 MID sequences) using 'Separate Reads by Barcode' from the Sequence menu
- Can split Polonator paired reads in half from using 'Set Paired Reads' from the Sequence menu
- The Geneious reference sequence assembler fine tuning option can be applied to existing contigs without needing to reassemble them
- BLAST:
- Custom BLAST databases created from sequences in Geneious will now store annotations and return fully annotated hits
- If Maximum Hits is set to 1 in Sequence Search, all results are downloaded to a single folder instead of creating many sub-folders
- Custom BLAST can now use multiple CPU cores (advanced option added)
- Blast hits now have a column in the document table listing the percentage of the query sequence covered by the hit
- Can view query centric alignments vertically compressed (like the 'Vertically Compress Contig' setting in previous versions)
- Full support for importing GFF 3 format annotations and better options for choosing which sequence(s) to annotate
- Trees can now be printed across multiple pages
- ACE format exporter for assemblies
- GC graph now has "frame plot" option to show GC content in each codon position
- Can resize chromatogram traces by dragging them up/down in the Sequence and Alignment Views
- Individual chromatogram traces (A,C,G and T) can be hidden in the Sequence and Alignment Views
- When viewing vertically compressed contigs/alignments, it shows sequence names even when zoomed out if there is only 1 sequence in the row within the visible region
- In an alignment view if you set a reference sequence then the statistics list the percentage of the reference sequence covered by other sequences in the alignment
- Tree view allows setting of a maximum length for tip labels, truncating longer labels
- Binning parameters can be set for individual folders or documents by turning on "Enable per folder/document binning" in the binning preferences
- Primer trimming now has a "Minimum Match Length" option, allowing better trimming of partial primers binding sites
- Go to next/previous disagreement button now skips over the middle of contiguous disagreements
- Sequence Searches now show up in Operations Table
- When assembler saves unused reads it puts unused paired reads in a separate list from unused unpaired reads
- SNP/Variation finder: Added option to not find variations or only find variations in regions covered by particular annotation types
New features:
- Reduced memory usage when importing big sequences, contigs, and alignments
Bugs fixed:
- Editing the consensus sequence in a contig/alignment doesn't modify the reference sequence now
- Fixed assembly sometimes introducing excessive gaps around regions that don't closely align
- Fixed Maq importer setting incorrect paired read expected distance on some contigs
- Numerous small bug fixes in Operations Table
- Fixed incorrect concatention of mixed quality and non-quality alignments
- Ace importer brings in sections of reads which fall outside the consensus
- Trim By primers matches primers partially off the end of a sequence
- Fixed base numbering on blasts that find hits on the reverse complement
- Fixed unresponsiveness when loading long sequences with many restriction sites into viewers
- Fixed bug introduced into multi-user chat in Geneious 5.1
- Max memory setting is now remembered when upgrading Geneious on Mac OS
Patch 5.3.1 (29 November 2010)
Bugs fixed:
- Fixed slow de novo assembly on gapped reads (bug introduced in 5.3.0)
- Fixed crash when trying to reorder a mixture of chromatograms and non-chromatograms in sequence/alignment view (bug introduced in 5.3.0)
- Fixed crash when saving enzyme sets (bug introduced in 5.3.0)
- Fixed 454 sff importer creating leading trim annotations 1 base longer than they should be
- Vector trimming no longer disables other trimming types when run at the same time
- When extracting a primer from the Annotations table, an Oligo sequence is correctly created
- If the options are wrong in document history there is now a button to display the saved xml
- Convert to oligo now correctly retains notes when run on multiple sequences
- ACE exporter now discards the reference sequence if one is present
- Fixed issues in Custom BLAST caused by sequence names containing underscores
- Editing the interval or calculated characteristics of a primer/probe is now disallowed in the sequence view
New features added in Pro version only:
- SNP/Variation finder: Added option to only find variations in regions covered by particular annotation types
- Coverage finder now merges regions where the coverage between them only slightly exceeds the coverage requirements.
Patch 5.3.3 (13 December 2010)
Bugs fixed:
- Fixed crash when using "File->Save As"
- Fixed crash when using "Find Variations/SNPs" on reference sequences with truncated CDS annotations
- Fixed bug where the Add Annotation dialog was crashing when you tried to add or modify intervals and qualifiers
- Variation/SNP finder: Merging of adjacent variations improved so that annotations are only merged as long as the variation is on the same subset of reads (with a small tolerance for read errors). Previously it would just merge all adjacent variants when the variant frequency was over 80%
- Fixed "Go to base" on big contigs causing hangs or running out of memory
- Fixed crash when assembling contigs to a reference sequence
- When assembling contigs containing paired reads to a reference sequence, for contigs that mapped to the reverse strand of the reference sequence, the paired distances were incorrectly set in the results
- Improved primer trimming to fix those cases where it fails to find some primers with mismatches or finds partial primers in the middle of the sequence when it shouldn't
- Updated the Java tools used to manage PDFs
- Fixed PDF documents imported into Geneious were not having their content indexed for search purposes
- Fixed bug in licensing where Geneious thinks a different user activated your license
- Fixed crash in SAM importer with reads starting with an insertion
- Fixed incorrect import in SAM importer when reads overlap the start of the reference sequence
New features added in Pro version only:
- Sequence/Alignment View: Can delete all selected annotations of a particular type
Patch 5.3.4 (20 December 2010)
Bugs fixed:
- Fixed crash in the Annotation table viewer"
- Fixed a crash in the GFF3 importer when parent is in a different sequence to child
- Fixed SAM Importer problem where reads were being imported offset from their correct position
- Fixed misc. licensing activation issues
Patch 5.3.5 (3 March 2011)
Bugs fixed:
- Fixed crash when using "Find Variations/SNPs" on contigs with trim annotations
- Fixed MySQL 5.5 compatibility issue in Shared Database
- Improved SOLiD csfasta import to include [.456] characters
- Fixed issue preventing the addition of custom NCBI databases
- Fixed bug in licensing when migrating hard drive
- Fixed issue where users on 64-bit Windows could not activate a license using 32-bit JRE
Patch 5.3.6 (8 March 2011)
Bugs fixed:
- Fixed a frequent crash that was introduced into the shared Database with v5.3.5
Version 5.1 (16 August 2010)
New features added in Pro version only:
- Primer browser - Used for choosing primers for testing and trimming. Allows sorting of primers and grouping them in to folders
- New batch rename with complex replacements and the ability to rename any field
- realign part of an alignment
- Virtual gel viewer now has labels above columns
- Extract PCR can now extract all PCR products or the product from any two selected primers
- GC content graph
- Fragment viewer and digest operation can now digest by each enzyme separately
- Assembler now uses multiple CPU cores for improved performance on multi-core machines
- Ligate Sequences can now be used to ligate a single linear sequence into a circular sequence
- Quality of bases in the consensus can now be calculated as a sum rather than max (more correct)
- Vector NTI gel archive importer (.ga4)
- Sequence view color schemes can now be completely customized
- Document history is now added for assemblies and sequence searches
- Can now add a sequence to an alignment without actually performing an alignment
- Automatic transfer of annotations to a reference sequence from BLAST hits or aligned sequences
- Can manually transfer annotations in query centric BLAST results to the reference sequence
- Can add annotations to sequences in 3D structure documents without needing to create a copy of the sequence
- Assembler now has a Stop button to get results before assembly finishes
- RNA Fold viewer now highlights selections made in other viewers
- Assembler now has Minimum Overlap and Minimum Overlap Identity options
- New distance matrix viewer for trees - includes display of patristic distances and matrix export
- Extract annotations has option to extract entire sequence when it contains a matching annotation
- High/Low coverage finder now has an option to only annotate coverage in genes/CDS regions and average the coverage over the gene
- Find variations/SNPs can now be run on the selected region only
- Digest Sequences now allows cutting at arbitrary selected positions
- Sequence view statistics panel now shows rough DNA melting point
- Annotations can now be modified by dragging the ends of them in the Sequence View
- Non-highlighted characters in an alignment can now be displayed as dots instead of fading their color
- Improved performance and reduced memory usage in both de novo and reference sequence assemblers
- Can assemble to multiple reference sequences
- Can save/generate consensus sequences directly from assembly instead of or in addition to conitgs
- SNP finder records the position of the SNP relative to the start of the CDS annotation it is in
- New assembler can now add sequences to an assembly and assemble sequences together
New features:
- "Operations" table shows the status of all currently running tasks and a history of recently run tasks
- Back Up button added to the toolbar with a greatly improved back up process
- Can now copy text out of annotation information popups in the Sequence View as well as click web links
- Ctrl+clicking (Mac OS: Command+clicking) on annotations allows selecting of multiple regions in Sequence View
- Nexus exporter has option to export simple form with no meta data (required by some other programs)
- The search index can now be paused by clicking on the indexing status on the bottom left
- Fixed issue where licenses bought in the same batch could think they were the same license
Bugs fixed:
- Several improvements to avoid path length limits on Windows systems
- Identity graph and other statistics now correctly ignore trimmed regions
Patch 5.1.1 (3 September 2010)
New features added in Pro version only:
- Improved de novo assembly algorithm to better handle assembly around repeat regions, particularly with paired reads
- Updated Commercially Available Enzymes from Rebase
Bugs fixed:
- Fixed crash when turning off annotations in the Sequence View after selecting an annotation
- Fixed crash when using live annotate & predict in Sequence View
- SFF importer now annotates trimmed regions
- Fixed bugs when changing the data location in the welcome dialog when doing a clean install
- Sequence View tooltips are now dismissed when you click on them
- Test with Save Primers - "Search for saved primers that match the selected sequences" now works
- Restore Backup in the File menu now works on folder type backups
- Fixed failure to save changes to a sequence after renaming or moving the folder which contains it
- Upgraded Lucene search indexing library used by Geneious which should fix indexing errors for some users
- Improved performance when indexing after modify lots of documents
- Sequence logo graph now ignores the reference sequence
- Searching in sequence/Alignment View now wraps around to start of the sequence if no matches are found
- Fixed crash when doing consensus alignment
- Fixed an issue where re-rooting an unrooted consensus tree would cause consensus support values to move to the wrong branch
- Tidied up and fixed various issues with the assembly report
- Fixed crash in dotplot when changing settings while data was being generated
- Improved operations table and fixed several issues
- Fixed excessive memory usage and performance issues when trimming sequences from the assembly options
- Improved performance when reference sequence assembling paired reads.
- Installers now do not require administrative privileges, instead requesting them on demand when a FlexNet license is activated in an environment where FlexNet isn't installed
- License activation works with proxies with spaces in their names
- Fixed crash when NCBI search is canceled
- Fixed bug in date setback detection
Patch 5.1.2 (15 September 2010)
New features added in Pro version only:
- Reference sequence assembler can now map reads that expand large introns as long as you increase the maximum gap size setting to an appropriate value
- Improved performance when importing millions of sequences
New features:
- Can delete local and remote jobs in Operations table
Bugs fixed:
- Reduced memory usage when doing reference sequence assembly
- Fixed bug where the number stating how many restrictions sites were found was incorrect
- Fixed crash sometimes when removing trimmed regions in alignment view
- Fixed crash when assembling a contig to a reference sequence
- Fixed odd behaviour in collaboration when two users start a chat to each other simultaneously, or one disconnects and reconnects
- Fixed bug where multiple single-user licenses bought as a batch were detected as the same license
- Tweaks to whitespace in GenBank flat exporter
- Fixed crash displaying Options in Document History if the plugin that created the Document is uninstalled
- MacOS X 10.4 (Tiger) now supports FlexNet licenses
Patch 5.1.3 (20 September 2010)
Bugs fixed:
- Fixed crash when trying to assemble blast results
- Fixed crash when deleting documents from the hit table of sequence search results
- Fixed crash when reference sequence assembling with 'Save contigs' turned off
- Fixed crash extracting manually-created primers from sequences
- Fixed crash digesting plasmid created from fragments with and without quality
- Fixed crash importing SAM file where soft clip overlaps consensus
- Fixed local blastx
- Fixed issue where fasta files are detected to be artemis files
- Removed use of -stable flag in MUSCLE
- Progress window is now displayed immediately when adding a custom blast database
Patch 5.1.4 (30 September 2010)
Bugs fixed:
- Fixed crash when viewing folders containing alignments or trees for some users
- Fixed crash selecting 'Transfer Annotations' in the sequence view of a BLAST hit
- Fixed crash when importing some unusually named sets of sequences
- Fixed assemble by name appending 'Contig' to the names of all generated contigs
- License activation uses port 80
- Fixed crash when doing tblastn
- Fixed crash importing ace file where first base in consensus is a gap
- Offer to replace end gaps with Xs when fasta exporting protein alignment
- Fixed GFF importer's base numbering off-by-one error
- "Design with Existing" for Primer Design no longer disabled when it shouldn't be
- Fixed an issue where Geneious could stay blank for a while after performing a full back up
- Fixed GUI hang when deleting jobs from remote services in operations table
Patch 5.1.5 (14 October 2010)
Bugs fixed:
- Fixed crash when assembling contigs that have trim annotations
- Fixed 'assemble by name' appending 'Contig' to the names of all generated contigs when saving results in sub-folder
- Fixed 'assemble by name' with empty assembly name prefixing contig names with numbers
- When assembling a few sequences the default was 'Highest Sensitivity' but if you didn't change it, it would do a 'Medium Sensitivity' assembly
- Fixed off-by-one error in annotations in GFF files with a sequence-region
- Fixed "No enzyme called... " occurring for some users when viewing nucleotide documents
- Fixed crash in SAM importer when cancelling from reference sequence file chooser
- Fixed crash displaying options when using "Insert into Vector" with an isnert sequence with very long overhangs
- Fixed persistent crash on startup when some one-month student licenses expired
- Fixed incorrect concatenation when a fragment had an extracted region that did not cover the entire fragment
- Fixed an issue where documents that contained non-ASCII characters could not be added to or retrieved from a Microsoft SQL Shared Database
- Fixed occasional crash in RNA Fold viewer
Patch 5.1.6 (19 October 2010)
Bugs fixed:
- If you grouped sequences into a list then edited the sequences in the list in the Sequence View, changes could get lost when restarting Geneious
- Fixed crash during NCBI search that starting happening due to a change at NCBI's end
- Fixed crash on startup that would disable Sequence Search
Patch 5.1.7 (3 November 2010)
Bugs fixed:
- Fixed failure to search UniProt databases due to change on UniProt servers
- Fixed a crash that could occur when importing a SAM file
- Fixed crash that could occur when deleting trimmed regions from reads
Version 5.0 (19 April 2010)
New features added in Pro version only:
- Paired end read support - For sequence assembly and Contig View
- Improved performance and greatly reduced memory usage on big contigs - Can view contigs of 10 million short sequences in 1GB of memory
- Split view - Open documents in multiple views and zoom levels
- Deleted items folder - Restore deleted documents (like Recycle Bin or Trash)
- Document history - Changes to documents are now recorded for later reference
- SNP/Variation finder for contigs and alignments
- Assembly maximum mismatches and maximum gaps settings are now percentages proportional to the sequence or overlap length instead of absolute values
- Virtual gel viewer
- RNA and Primer secondary structure prediction and visualization (uses RNAfold)
- Import and view gel image files
- MAQ alignment format importer
- CAF assembly format importer
- SAM format importer
- FastQ format exporter
- Qual format exporter
- Can sort sequences in an alignment by the bases or residues at a particular position
- Option to specify the minimum confidence (ie. quality) for a call to be made in the consensus sequence
- When a consensus sequence is extracted or generated it will retain calculated quality scores
- High/Low Coverage finder for contigs and alignments
- Non-cutting enzymes are now added to the "Restriction Sites" table when "Find Restriction Sites" is used
- Added shared Database administration interface
- Export images to EPS format
- Basic microsatellite data support (includes .fsa format import and viewer)
- View settings in the sequence view can be saved as preset profiles
- Dotplot now synchronizes its selection with the sequence view
- Keyword filtering in the "Annotations" table view
- Can now add annotations to the consensus sequence in an alignment
- Find in translation for nucleotide sequences in the Sequence View
- Find duplicates can now find duplicates in alignments and sequence lists
- Batch rename now works on alignment and sequence lists
- Concatenate now works on sequence lists
New features:
- Can now re-root rooted trees in Tree View
- View preferences can now be stored separately for each document in the sequence view
- New controls layout in the sequence view
- Fragment length is shown when one restriction site is selected and the mouse is moved over another in the sequence view
- Added buttons and shortcut keys to the Sequence View to go to the next/previous annotation of the same type
Patch 5.0.4 (14 July 2010)
Bugs fixed:
- SAM importer 30 - 50 times faster
- Fixed a few small bugs in SAM importer
- Better progress for custom BLAST and ClustalW alignment
- VNTI importer can import files with empty motifs, subbases with characters illegal in file names, and notes with different fields to existing ones
- Fixed trimming incrrectly annotating primer and vector hits when trimmed regions are removed
- Pir importer can import files using dot as gap chracter
- Fixed hang when Geneious regains focus on Pfam panel
- Fixed occasional crash when selecting a region in the sequence/alignment view
- Fixed compatability with Microsoft JDBC driver
- Fixed an issue where a small number of documents are hidden when initially viewing a folder if that folder contains more than 250 documents
- Addressed issues with large option windows on low resolution screens
- Notes can now be shown on tips in the tree view again
Patch 5.0.3 (8 June 2010)
New features:
- Can have the pipe character "|" displayed for identities in the text view for pairwise alignments and blast hits (Advanced options in General Preferences)
Bugs fixed:
- Fixed crash sometimes after saving changes to a contig or alignment
- Fixed sequence/contig/Alignment View displaying the original name instead of the current name for some sequences.
- Some icons were missing when running Geneious using Java 5
- Generating a consensus sequence from a contig ignored the 'Assign Quality' setting if the reference sequence had no quality
- Fixed crash during de novo assembly of sequences containing too many ambiguities
- Fixed a bug in the generation of assembly reports when assembly from existing contigs
- Sequences with quality but no chromatogram trace no longer have the chromatogram icon (eg. extracted consensus sequences)
- Fixed crash when concatenating or ligating some types of sequence list documents.
- Fixed Sequence View not displaying some graphs (e.g. CpG Islands) because it wrongly thought the sequence had been edited
- Extracting a sequence can no longer result in partial restriction sites or primer binding sites
- Fixed annotations appearing 1 off from their correct location when extracting a region from an alignment starting with a gap
- Fixed a bug that caused   to appear in the export of BLAST alignments in traditional BLAST text format
- Fixed crash aligning a sequence consisting entirely of gaps
- Improved memory efficiency, progress reporting and cancellability of the SAM importer
- Fixed GenBank importer to recognise recognition sequences on enzyme annotations exported from Geneious
- Fixed crash concatenating sequences containing quality but no traces
- Insert into Vector recognises cut sites that have amibiguities or have direction when they shouldn't
- Better error reporting for FlexNet licenses including trials
- Vector NTI importer ignores files starting with ._
- Fixed local documents reindexing your entire database sometimes when you restart Geneious before it finishes indexing
- Extract PCR Product now works on sequences where primer annotations are right on the end.
- Fixed the alignment of text in the blast text view on certain systems
Patch 5.0.2 (17 May 2010)
New features:
- Reference sequence assembly now makes use of multiple CPUs. And de novo assembly makes better use of multiple CPUs
Bugs fixed:
- Fixed generate consensus sequence operation in the tools menu putting annotations on the consensus sequence in the wrong place in the generated consensus sequence
- Manually created trim annotations directly adjacent to other leading/trailing trim annotations are now recognized as trim annotations
- Fixed bug where if you trim in the assembly options and are using a reference sequence, the reference sequence gets included twice in the contig
- Fixed crash generating consensus sequence when using the ignore gaps setting
- Fixed sorting sequences in the sequence/alignment crashing sometimes after deleting sequences
- Fixed crash when assembling from a mixture of paired and unpaired sequences
- Fixed crash when reverse complementing some contigs
- Sequence logo graph now ignores regions covered by trim annotations
- Fixed custom assembly options not remembering your preferred settings for next time you do an assembly
- Fixed Geneious crashing on startup sometimes
- Turned off per-document settings in the sequence view by default (can be changed under Appearance & Behaviour tab in preferences)
- Annotations on the consensus sequence were put in the wrong location when "Hide gaps in reference sequence" was on
- Fixed Contig View bug where consensus and reference sequence were sometimes not rendered when using the paired distance color scheme
- Fixed Contig View where differences weren't highlighted when using some color schemes or when something was selected
- Fixed reference assembly bug causing some reads to be incorrectly aligned to the reference sequence or occasionally crashing.
- Translation alignment works on local alignment
- Trial activation fixed for 32-bit Linux
- Updated the Sample Plasmids from NEB
- Fragment length column added to enzymes table
- Artemis importer now imports "sequence only" format
- Fixed some crashes in the SAM importer
- Geneious format export now preserves additional data such as document history and per-document settings.
- Viewers now display documents in the same order as the document table
- Consensus sequence now always ignores end gaps on a "free end gap" alignments (ignore end gaps option removed from consensus)
- Shift+Backspace now permanently erases a document/folder on Mac OS
Other:
- Per-document settings turned off by default in Sequence/Alignment View
Patch 5.0.1 (29 April 2010)
New features:
- FastQ importer can now import directly from compressed .fastq.gz files
Bugs fixed:
- Fixed Paired-read de novo assembly not fully using paired-read information
- Fixed "restore defaults" button in assembly options not restoring correct defaults
- Fixed printing circular sequence views
- Fixed crash when using shared Database
- Fixed sorting sequences in the sequence/Alignment View not working or crashing
- Fixed Sequence View hanging viewing long reference sequence contigs with under a thousand sequences with quality
- Fixed crash generating consensus sequences in alignments/contigs which have columns of all gaps
- Fixed bugs in SAM importer
- Fixed crash when using similarity color scheme on contigs with trim annotations
- Fixed occasional crash when starting to build an alignment
- Fixed crash when vector trimming
- Fixed crash doing restriction analysis
- Fixed missing task buttons at top of primer design options
- Fixed CAF importer bugs
- Stopped Geneious trying continuously to import sample documents when something goes wrong.
- Fixed failure to import some nexus documents.
- Stopped separate windows viewing the same document from synchronizing their selections unless you turn on a split view
- Fixed sequence/Alignment View crash when clicking "find previous" in the find window
- Fixed MAQ importer incorrectly importing quality values
- Find Motif now strips invalid characters from the motif to find
- Batch export now warns if there are documents with the same name instead of silently overwriting documents with the same name
- Various document history bug fixes and improvements
- Fixed collaboration crash when sharing two or more folders with the same name
- Fixed crash importing some files containing 10,000 or more sequences
- Fixed bugs to do with annotations on the consensus sequence of an alignment
Version 4.8 (29 October 2009)
New features added in Pro version only:
- Fast de novo assembly - Capable of assembling 100,000 454 reads or 500,000 Illumina Solexa reads without a reference sequence in a few minutes on a desktop machine.
- New dotplot - capable of dotplotting genome sized sequences with brand-new controls (utilizes EMBOSS)
- Better handling of next-gen sized data - greatly improved speed and memory efficiency when dealing with large next-gen data sets
- Primer extension support - add a restriction site or other extension to primers and Geneious takes this in to account when testing the primer and using it for other analysis
- Trim by primers - screen for primers from the local database
- Batch export - export several documents to separate files in one step (File > Export > Batch Export)
- Color sequences according to their annotations ("By Annotation" option under Colors in the Sequence View)
- More powerful primer design on alignments and support for designing primers on assemblies
- FastQ file format import
- CsFasta file format import
- Qual file format import
- Add and Remove enzymes from enzyme sets and combine enzyme sets
- Search for individual primers from your database that match a sequence
- Option to find residues in the translation of DNA (Edit > Find in Document)
- Quality measures for chromatograms added to sequence view statistics (Confidence and Expected Errors)
- Extinction coefficient for proteins added to sequence view statistics
- Read length and coverage statistics for sequencing data added to sequence view statistics
- Sort sequences by name and other attributes in sequence lists, alignments and assemblies (right click in Sequence View and under Properties options)
- The EMBOSS tools plugin is now included with Geneious as standard (adds many functions)
- All models in a 3D structure can now be shown simultaneously in the 3D structure view
- Folders can now be copied between server and local database by drag and drop
New features:
- Pan in Sequence View by holding Ctrl+Alt while dragging (Command+Alt on Mac OS)
- Greatly improved local database start up time for users with large numbers of documents (takes effect after first start up of 4.8)
- Geneious export no longer offers compressed/uncompressed format, Geneious format is always compressed with .geneious extension
- Sequence view statistics can now be copied to the clipboard
- Improved display of multi-interval annotations and primers in the sequence view
Bugs fixed:
- Change residue numbering now works on circular sequences
- Notes can now be stored in the Shared Database
Patch 4.8.5 (4 March 2010)
Bugs fixed:
- Updated BLAST code to reflect recent changes to NCBI's output format- fixes BLAST
- Speed up loading of large documents in dotplot
Patch 4.8.4 (10 February 2010)
New features:
- Annotation generators which act on chromatograms now work on alignments and lists containing chromatograms
- More memory efficient indexing of documents and better handling of low memory when indexing
- Improved behavior of dotplot on blast hit documents
Bugs fixed:
- Fixed crash that was preventing NCBI blastx from working
- Referenced sequences are now retained on assemblies of up to 10,000 sequences
- GenBank importer now works on files with nonstandard indentation of base numbers
- Fixed crash when concatenating chromatogram and non-chromatogram sequences
- Fixed crash when trimming while assembling with a blast hit
- Alignments with many referenced sequences are now saved more quickly
- Fix sequence search crash when query sequence name is not a valid folder name
- Fixed crashes caused by reverse direction annotations on protein sequences (when sequence searching, copying or extracting)
- Fixed an issue for some 32-bit linux users where Geneious wouldn't start
- Fixed crash in primer design when working with an alignment containing both chromatogram and non-chromatogram sequences
- Fixed crash caused by removing sequences from an assembly or sequence list which have been used for another assembly
- Primer design and testing now ignores regions of ?'s (eg. missing regions in genomes)
- Vector NTI importer no longer fails on files with a period in field values
Patch 4.8.3 (18 December 2009)
New features:
- Option to search on either forward or reverse strand in Search for Motifs
Bugs fixed:
- Extract PCR Product no longer adds one incorrect additional base
- Fixed Geneious giving out of memory errors when reaching about 80% of the memory it should be able to use in 64 bit versions
- Correct extension is now listed on reverse primers which are added via Test with Saved Primers
- Fixed crash when undoing in the Sequence View
- Fixed hang on startup
- Fixed crash when saving changes to an alignment/contig
- Fixed hang when saving changes in an alignment/contig
- Fixed crash after deleting all sequences from a blast results folder
- Fixed crash when viewing chromatograms corrupted by a bug in earlier versions of Geneious. The corrupted chromatogram data is partially recovered in Geneious 4.8.3.
Patch 4.8.2 (30 November 2009)
Bugs fixed:
- Fixed a bug that caused Smart Agents to become normal agents after restarting Geneious
- Reduced memory usage for sensitivity based denovo assembly
Patch 4.8.1 (25 November 2009)
New features added in Pro version only:
- Reference sequence assembly option to randomly choose between best multiple matches
Bugs fixed:
- Memory leak when viewing sequence search results
- Out of memory error when saving changes to large contigs
- Correctly handle extracting annotations with multiple intervals in different directions.
- Query centric view no longer incorrectly splits annotations apart when hide gaps in reference sequences is on
- Removing bases when trimming on alignments no longer unaligns the sequences being trimmed.
- Fixed crash and/or incorrect results when building several alignments or trees simultaneously.
- Primer design on circular sequences now correctly finds primers for regions spanning the origin
- Fixed incorrect rendering of annotations spanning the origin of circular sequences when zoomed out
- Fixed crash when restriction sites are found spanning the origin of circular sequences
- Fixed crash when editing a contig immediately after reverse complementing the entire contig
- Find in sequence and find motif now find sequences spanning the origin of circular sequences
- Document fields such as description are now preserved in an alignment built from a sequence list
- Fixed bug printing a zoomed in sequence view where it would zoom out under some conditions
- And a few other minor bug fixes
Version 4.7 (29 June 2009)
New features added in Pro version only:
- Query centric multiple alignment BLAST view - Every BLAST search now has a view tab with the query centric alignment
- Fast reference assembly - Can now assemble 100,000 reads to a reference in less than a minute
- ContigExpress (.cep) import
- Primer database - Select primer sequences from anywhere in your databases for testing
- 454 import and handling - Import SFF files then view and assemble the sequences to a reference
- Custom keyboard shortcuts - Choose a shortcut key for just about any action in Geneious (Preferences > Keyboard)
- Show translation by coding annotations or just for the selected region
- Translate alignments/contigs relative to the start of alignment or the consensus sequence
- Set a reference sequence in an alignment/contig and highlight disagreemets etc versus the reference sequence (right-click > Set as reference sequence)
- Change the font and style for selected taxa in the tree view
- Color nucleotide triplets by their translation
- New tabular view of annotations on sequences
- New view showing graph of sequence lengths
- Extract PCR Product operation added
- Automatic scaling of chromatogram height
- Sequence view remembers zoom level for next disagreement and Editing state for assemblies
- Original chromatogram files can now be exported even after editing a chromatogram
- Can now trim the consensus to the reference sequence (if present)
- Find ORFs and structure prediction now works on alignments
- Improved coverage graph - stays after editing and can highlight low coverage regions
- Improved contig view - can vertically compact the contig view so that multiple reads can appear in the same row
- Consensus alignment has option to create an alignment of the consensus sequences only (useful for comparing assembly results)
- Option in BLAST to fully annotate the hit summaries - eg feature annotations, taxonomy and other properties
- Option to design a reverse primer only added
New features:
- MacClade color scheme added
- Can select multiple regions simultaneously in the Sequence View (by ctrl-drag selecting successive regions)
- Improved sequence/alignment/Contig View performance. Can view contigs with 100,000+ reads
- Improved performance handling large numbers of sequences - Imported sequences are grouped into a single list document and existing sequences can be grouped manually
- Check for Updates Now added to the Help menu and General Preferences
Bugs fixed:
- Fixed long delay before results appear when a large operation is completed
- Other columns such as description and organism can now be consistently used as labels in tree and sequence view
- Distance matrix now shows up more consistently in Text View on tree building results
Patch 4.7.6 (22 September 2009)
Bugs fixed:
- Added support for Mac OS X 10.6 (Snow Leopard)
- Printing: Fixed the positioning of the Middle line of text view of BLAST alignments
- Query Centric Alignment: Query is not annotated
- Primers: Determine characteristics and testing are using default minimum GC
Patch 4.7.5 (6 August 2009)
Bugs fixed:
- Vector NTI import now retains user defined fields for all sequence file types
- Importing a file containing a single sequence no longer asks whether to create a sequence list
- Save as image file fixed for the sequence view
- Fixed crash when deleting bases across the origin on circular sequences
- License is now correctly loaded from a file if the free trial is still active
- Fixed issue when copying large files to Microsoft SQL shared Database
- Fixed issue where extracting a region from a circular sequence wouldn't produce a sequence
- Fixed issue where the selection would move erratically on circular sequences
Patch 4.7.4 (22 July 2009)
Bugs fixed:
- Extract now offers to reverse complement if an annotation on the reverse strand is selected
- When importing sequences Geneious now asks whether to import as a sequence list or individual sequence documents
- Fixed incorrect downloading of genomic contigs from NCBI (due to not reverse-complementing when necessary)
- When extracting primers and pcr products Geneious now asks what to do when the primer doesn't match the sequence perfectly (eg. when there is degeneracy)
- Google Scholar links in pubmed articles now work more effectively
- Built-in tutorial and sample documents updated
- Fixed primer design on RNA sequences
Patch 4.7.3 (16 July 2009)
New features:
- Zoom to a region by holding Alt and dragging the mouse in the Sequence View
Bugs fixed:
- Fixed sequence view occasionally discarding changes when saving when editing multiple large documents simulaneously
- Fixed an occasional crash when clicking undo in the sequence/Alignment View
- Fixed intermittent crash when assembling reads
- Fixed an occasional crash when deleting results from a sequence search
- Primers: Design with existing now works with heavy degeneracy in target sequence
- Primers: Performance of testing degenerate primers improved
Patch 4.7.2 (8 July 2009)
New features added in Pro version only:
- Can now test all primers in your database against a sequence
New features:
- Added the ability to rename, remove and reorder sequences in a sequence list
Bugs fixed:
- Fixed stuck tooltips when switching to another program on Mac OS
- Fixed a bug that could cause a crash when searching the local database with an empty field
- Fixed a hang that could occur in a shared Database
Version 4.6 (9 March 2009)
New features added in Pro version only:
- Gateway Cloning support - Add attB sites, perform BP and LR reactions
- Vector NTI database importer - Import all supported data types from a Vector NTI database in one step
- Assemble by name - Use names to assemble many groups of sequencing reads in one step
- Sanger GFF Import and Export - Attach annotations from a GFF file to a sequence or export annotations from any sequence to GFF
- Ability to change font sizes in the Sequence View
- Overlay annotations on the bases in the Sequence View
- Import Rebase proto and withrefm fromats
- Binning of traces and assemblies according to quality indicators
- Ability to save save assembly results to a new folder with a permanent report document
- Ability to edit the consensus sequence in the Sequence View
New features:
- An option to flip the tree view horizontally
- Purine vs Pyrimidine color scheme
Gateway is a registered trademark of Invitrogen Corporation
Patch 4.6.5 (19 June 2009)
Bugs fixed:
- Fixed a bug that caused incorrect NCBI Gene documents to be downloaded in some cases
- Fixed a bug that could cause a crash when searching the local database with an empty field
Patch 4.6.4 (5 May 2009)
Bugs fixed:
- Fixed a bug that caused tutorials to be imported with a page missing
Patch 4.6.3 (4 May 2009)
Bugs fixed:
- Fixed a bug where only the first 1400 bp of sequences were imported from Vector NTI archive files
- Fixed bug that prevented the loading of documents with special characters in the shared Database
Patch 4.6.2 (20 April 2009)
Bugs fixed:
- Fixed hang when starting up Geneious after trial license expires
- Fixed bug where vector contamination at end of sequence was not detected during trimming
- Fixed local blast file setup on Linux
- Vector NTI importer now correctly imports dates and multi-line comments
- Fixed crash in "Add database" when using Geneious Basic
- Alignment concatenations now have correct names for sequences
- Fixed crash when previewing "Save to image" for very large images
- NCBI no longer warns about ambiguous bases once for each sequence in batch search
Patch 4.6.1 (31 March 2009)
Bugs fixed:
- Fixed issue where the Sequence View would not display quality information on a sequence with no trace in a contig.
- Fixed the EndNote importer.
- Improved the performance of the GFF importer
- Fixed an issue where the BLAST plugin was not compatible with some custom WWWBlast servers.
- Improvements to sequence editing.
- Improved splash screen :D
Version 4.5 (27 November 2008)
New features added in Pro version only:
- Unified Sequence Search - New BLAST searching interface including batch searching and improved handling of results
- New 3D Structure View - Includes ability to select parts of a structure and modifying their appearance individually
- Real-time Restriction Analysis and ORFs - Find restriction sites and ORFs are now part of the Sequence View allowing real-time updating of sites as options are changed
- Similarity Color Scheme - New color scheme which colors residues in an alignment according to similarity
- Support for Sassafras K2 license servers
- Print just the visible region from the Sequence or Alignment View
- Added support for designing sequencing primers
New features:
- Send Feedback / Report Bug - New item in the Help menu to easily send us your comments or report a bug
Bugs fixed:
- Fixed issue where File -> Save As would delete Notes from a document
- SCF import now handles a wider range of files
- Fixed problems with corruption of trees when sequences are renamed in the alignment
Patch 4.5.5 (10 March 2009)
Bugs fixed:
- Fixed wrong genomes being downloaded due to NCBI changing their format
- Made NCBI server location updatable
Patch 4.5.4 (22 January 2009)
Bugs fixed:
- Fixed crash when assembling contigs
- Fixed bug where importing large Geneious databases would run out of memory
- Fixed clustal alignments not storing references to original sequences
- Fixed crash when viewing sequences with a large font size
- Fixed changes made to imported Newick trees (e.g. coloring nodes) being lost after restarting Geneious
- Fixed changes made PopSet documents being lost after restarting Geneious
- Fixed very slow performance viewing some contigs
- Fixed crash and occasional incorrect dates when searching NCBI's SNP database.
Patch 4.5.3 (22 December 2008)
Bugs fixed:
- Fixed a bug that could cause the Text View to crash and corrupt the search index
- Identical foreground and background colors in the similarity color scheme no longer cause a crash
- Setup of COGS BLAST will no longer crash when the NCBI plugin is disabled
- Send Feedback / Report Bug now uses the standard HTTP port
Patch 4.5.2 (16 December 2008)
Bugs fixed:
- Restriction site annotation generator respects enzyme set document
- Fixed unresponsiveness while loading large sequence in Sequence View
Patch 4.5.1 (12 December 2008)
Bugs fixed:
- Fixed memory leak when repeatedly viewing sequences in Sequence View
- Many other small fixes
Version 4.0 (5 September 2008)
New features added in Pro version only:
- Cloning operation - Insert into vector provides one-step insertion into a plasmid
- Plasmid maps - restriction sites and annotations on circular sequences are now shown with the label pointing to the region
- Tree coloring - branches and labels can now be colored in the Tree View
- DeCypher - Added support for searching using TimeLogic's DeCypher accelerator hardware
New features:
- Annotation Viewing - Labels are positioned intelligently outside of region markers at low zoom
- Quality information is now imported from .ace files if available
- Chromatogram quality values are displayed in the Text View
- Save As... (Ctrl+Shift+S) added to File menu
- Protein structures now display all amino acid and DNA sequences
- New sample documents
- PopSet results now downloaded in sets
- Added more annotation types with improved coloring
- Annotations downloaded from GenBank are given more informative names
Bugs fixed:
- Further improvements made to chromatogram import to support a wider range of files
- Annotations are now displayed correctly on sequences from NCBI Gene (broken by changes at NCBI)
- Fixed situation where residues may be highlighted as agreements incorrectly
- Disulfide bond annotations from UniProt are now displayed correctly
- Geneious will no longer create dummy drives on Mac OS if a network drive is disconnected
- Advanced search for Pfam now works
- It is now possible to design primers to surround a single base as the target
Patch 4.0.4 (31 October 2008)
Bugs fixed:
- Changed NCBI SNP service to use new XML format
- Upgraded Pfam to revision 23
Patch 4.0.3 (16 October 2008)
New features:
- It is now possible to limit by Entrez query when doing a BLAST search
Bugs fixed:
- Fixed some issues with upgrading from previous versions
- Fixed a bug that caused a failure to load or import some chromatograms that were valid before Geneious 3.8
- Can now import chromatograms that contain any ':' or 'S' characters
- Fixed display problems caused by the latest Java update on Mac OS
- Reduced text size in Text View of Pubmed documents
- Corrected residue numbering for blastx results to be of the translation rather than the nucleotide query
Patch 4.0.2 (17 September 2008)
Bugs fixed:
- Made it possible to edit and manually add primer annotations again
Patch 4.0.1 (15 September 2008)
Bugs fixed:
- Add annotation in the Sequence View now remembers last type used
- Improved layout of labels in circular and linear Sequence View
- Improved Sequence View responsiveness
Version 3.8 (30 June 2008)
New features added in Pro version only:
- GenBank flat and XML exporters - For all nucleotide and protein sequences
- Text view on GenBank documents - For sequences under 10K in length, the full GenBank flat record is provided as the text view
- Vector screening - "Trim Ends" lets you trim for vector contamination
- Support for sticky ends - restriction digest produces documents with sticky ends, and concatenation takes these into account
- More sample restriction enzymes sets - Blunt, 3', 5' and common enzyme sets
- Restriction analysis improvements - Find enzymes not cutting a sequence, and restrict the search for restriction sites to those that do not cut within a certain region
- Extract annotations - inverse - You can extract all regions of a sequence not covered by an annotation
New features:
- Sample NEB plasmids - Annotated plasmids from the NEB website are included in the sample documents
- Concatenation into circular sequence - Concatenation can preserve the origin of a concatenated circular sequence fragment
- Selected document count - status bar in document table informs you how many documents are selected
- Go To Position in sequence - Jump to a particular index in a sequence, or select a particular range
- Improvements to annotation rendering - New 3D look and other improvements
- Performance improvements in the sequence/Alignment View
Bugs fixed:
- Go to next disagreement no longer prompts to save
- Undo in the sequence/alignment editor no longer causes crashes
- Primer design correctly evaluates all possible mismatches
- Shared Database monitors external changes to documents being viewed
- Many other small fixes
Patch 3.8.5 (14 July 2008)
Bugs fixed:
- Fixed crash when encountering invalid NCBI files which have no division
Patch 3.8.4 (10 July 2008)
Bugs fixed:
- Fixed N's being imported as M's for ab1 trace files
Patch 3.8.2 (8 July 2008)
Bugs fixed:
- Fixed failure to import some chromatograms and fixed crash when trying to view some chromatograms imported using previous versions of Geneious
- Fixed crash when translating annotations in some circumstances.
Patch 3.8.1 (4 July 2008)
New features
- Windows 64 bit distribution to allow you exceed the 1.5 GB maximum memory limitation of 32 bit systems.
Bugs fixed:
- GenBank flat importer: No longer strips the last character from each keyword
- Tree Builder: Now produces unrooted (instead of rooted) consensus from unrooted samples
- Shared Database: Saving changes to documents in some cases no longer reverts to displaying the previous version of the document
- Sequence logo graph: Fixed crash when viewing alignments of proteins containing stop codons.
- Find duplicates: Fixed crash when finding duplicates on some documents
Version 3.7 (6 May 2008)
New features added in Pro version only:
- Protein Statistics - Real time update of isoelectric point and molecular weight in the statistic section of the Sequence View.
New features:
- Plugin Manager - Download and install plugins from within Geneious and stay up to date with the latest plugin releases.
Patch 3.7.1 (29 May 2008)
Public API issue resolved, no functional difference to 3.7.0
Version 3.6 (13 March 2008)
New features added in Pro version only:
- Vector NTI Import - Including molecule, oligo, enzyme and citation archives as well as sequences (.gb/.gp) and alignments (.apr).
- Edit tracking - annotations are automatically created which record what residues have been changed.
- Coverage graph for alignments and contigs
- Convert sequences between RNA and DNA - Under the Sequence menu
- Strip alignment columns - An operation in the Tools menu to remove all columns containing only agreements/transitions/gaps from an alignment
- Sequence View: can now highlight agreements with the consensus. Can also highlight transitions and transversions from the consensus.
- Sequence View: Can now jump to next agreement/disagreement/transition/transversion.
- Sequence View: Fill from left - Hold down the alt key when deleting regions (or individual bases) to move bases to the left (instead of those on the right) into the deleted region
- Sequence View: Can now choose colours for annotation types (click on colour box)
- Universal Mac OS binaries added for Primers and MUSCLE - improved performance on Intel Macs
New features:
- Improved tutorial with links to extra information
- Main menu structure improved
- Dotplot shows dotplot of one sequence with reverse complement of another
- Clustal color scheme added to sequence view
- Documents can now be sorted by their read/unread status
Patch 3.6.2 (28 March 2008)
Features added:
- Added support for Clustal 2.0
Bugs fixed:
- Fixed a couple of residue numbering bugs in PDB documents
- Annotations are no longer turned on every time a document is edited
- A small number of users who upgraded were not able to start the new version of Geneious
Patch 3.6.1 (19 March 2008)
Bugs fixed:
- Annotations from NCBI Gene are now added correcly
- Ambiguous base codes are now translated correctly
- Muscle executable fixed for PPC Macs
- Assembly can now handle assembling U (uracil) to T (thymine)
Version 3.5 (25 October 2007)
New features added in Pro version only:
- Motif finding - Select Edit -> Find in Document... and use Annotate All
- Muscle Alignment - Available in the Alignment options window.
Based on the state of the art alignment program Muscle.
- Shared Databases - Store documents in a central and secure relational database, mutliple users
can work on the same data simultaneously.
- Linnaeus Blast - Evolutionary view of BLAST results. Select Tools -> Linnaeus BLAST...
- Degenerate primer design - Select an alignment and select Tools -> Primers -> Design Primers...
- Extract annotations - Searches a sequence for annotations matching your criteria and extracts them.
Select Sequence -> Extract Annotations...
- Consensus alignment - Align several alignments using the consensus sequence. Available in the
Alignment options window
- Improved trace trimming - Trimmed ends are kept for adjustment after assembly.
New features:
- Sequence view improvements - Graphs now stay in view always and the names are resizable.
- Preferences now stored in user's data directory - Preferences will not be lost when accessing data on a network drive from different computers.
- Added support for amino acids U and O (Selenocysteine and Pyrrolysine)
- Improved dot plot - Added a crosshair
Patch 3.5.6 (19 December 2007)
Bugs fixed:
- Fixed corruption of chromatogram data due to editing.
- Editing of note types now behaves correctly
- Can now create Pfam sequences from UniProt sequences
- Default memory setting for MUSCLE alignment is now correct
Patch 3.5.5 (30 November 2007)
Features added:
- Geneious now runs on Solaris 10! Some plugins using native code only work on x86 systems.
Patch 3.5.4 (22 November 2007)
Bugs fixed:
- NCBI blast: tblastx hit annotation is now in the right direction!
- Ignore gaps is now disabled when using highest quality consensus
- The alignment dialog ran off the screen with too many alignment methods
- Endnote files were not importing correctly
- Various bugs in the shared Database plugin relating to referenced documents
- The shared Database plugin now automatically sets up schema in database
- The GenBank importer now supports files from GeneSNPs database
Patch 3.5.3 (15 November 2007)
Bugs fixed:
- Improved support for customers whose license no longer allows free Pro upgrades
- Can now edit phylogeny documents
- Fixed crash when phylogeny document referenced alignment document that had sequences removed.
- Fixed hang when saving to PDF
- Fixed various bugs relating to the shared Database plugin
- Fixed some memory leaks
Patch 3.5.2 (1 November 2007)
Bugs fixed:
- Various crashes in the shared Database plugin
- Find in annotations on a sequence crash
Patch 3.5.1 (29 October 2007)
Bugs fixed:
- Temporarily hid shared Databases from agents and collaboration for
stability
- Memory leaks in some viewers
- Crashes in some viewers
Version 3.0 (13 April 2007)
Features added in Pro version:
- Contig assembly!
- Circular Sequence View!
- Restriction Site Identification!
- Improved primer design including mismatching and testing multiple primers!
- Enhancements to the Sequence View including viewing of translation and complement alongside sequences
- Sequence logo graphs
- Improvements to the Tree View including collapsible subtrees
- Nucleotide alignment via translation and back
- New file importers: PIR, EMBL, GCG and Phylip
- PFAM database
- Remove duplicates function on downloaded documents
- Extensions to options available in Structure View
- Local folders can now be moved (File -> Move Folder... or drag and drop)
- Highest quality base consensus
- Geneious users can chat with users of other Jabber clients, e.g. Google Talk
- Plus lots of minor features and improvements
Patch 3.0.6 (16 July 2007)
Features added:
- Better management of multiple concurrent user licenses
Patch 3.0.5 (04 July 2007)
Features added:
- Support for multiple concurrent user licenses
- Support for licenses with arbitrary periods
- Support for licensing all users on a computer
Bugs fixed:
- A workaround for a bug in Apple's tree implementation
- Changed an invalid reference in the tutorial
- Made the E-value column leftmost by default
- Provide option to not print circles on nodes in tree view
- Various bug fixes
Patch 3.0.4 (15 May 2007)
Bugs fixed:
- Crash installing plugins
- Profile alignment crash
- Contig assembly crash
- Problem translating sequences with single residue annotations
- Other bug fixes
Patch 3.0.3 (27 April 2007)
Bugs fixed:
- Crash when editing chromatogram alignments
- Crash when viewing chromatograms without quality information
Patch 3.0.2 (24 April 2007)
Bugs fixed:
- Crash disconnecting after chat
- Chromatogram document crash
- Crash when viewing trees renamed in 2.5
- Other bug fixes
Patch 3.0.1 (18 April 2007)
Bugs fixed:
- Crash deleting two sequences from an alignment
- Cannot download PFAM database files when there is an active smart folder
- Atom filtering broken in 3D Structure View
- Saving notes on a large number of documents is slow
- BLAST search failed due to a change at NCBI
- Other bug fixes
Version 2.5 (13 November 2006)
Features added:
- NCBI BLAST agents
- Ability to specify advanced options to NCBI BLAST.
- Ability to change location of NCBI BLAST server.
- Sequence View: sequence names for alignments are now always visible (if the show names preferences on) even when scrolled to the right.
- Sequence View: option to display the original sequence residue position numbers in alignments and extracted sequences.
Includes displaying the original sequence residue numbers for local alignment results.
- Sequence View: can handle alignments of 10,000 sequences, and individual sequences up to 100 million residues in size.
Performance also improved on smaller sequences and alignments. (Documents over 100Mb only supported by Pro version).
- Geneious can handle larger documents than previous versions and displays a progress bar when loading individual large documents.
- MEGA importer
- PHRAP (ace) importer
- GenBank flat file, GBSeqXML and INSDSeqXML importers
- Export table values as CSV file.
- Improved printing support. Print preview, with various options.
- Improved saving to PNG support with preview and various options.
- Improved Dotplot View: Now much faster, especially for low stringency setting.
- Support importing / exporting .geneious files in zip compressed format, to save disk space.
Features added in Pro version:
- Primer design (This product includes software developed by the Whitehead Institute for Biomedical Research)
- Collaboration: Contacts can browse shared folders like their local database.
- Collaboration: Similarity (blast-like) search contacts.
- Collaboration: Chat with contacts.
- DNAStar .seq and .pro importer
- Teaching Module, allows users to create HTML tutorials for their students which link in with Geneious documents.
- Smart folders: Folders that can sort documents according to relevance to a subject.
- Can save document views to PDF and SVG images.
- Sequence View: can reorder sequences and remove sequences from alignments
- Sequence View: option to display residues the same as the consensus sequence as either "." or without any color.
- Geneious alignment can automatically detect sequence direction
- A gui interface for installing and un-installing plugins.
Bugs fixed:
Patch 2.5.4 (15 January 2007)
Bugs fixed:
- Geneious alignment crashing on sequences containing uracil (U)
- Geneious crashing on startup when two copies of the same plugin installed
- Printing on Mac OS X uses native options. Resolves several problems
Patch 2.5.3 (29 November 2006)
Bugs fixed:
- Primers in menu not working for 3 or more sequences
- Fasta exporter randomizes order of sequences in alignment
- Various stability bugs fixed
Patch 2.5.2 (17 November 2006)
Bugs fixed:
- Fixed issue where new users were not able to access a new Pro version trial.
Patch 2.5.1 (16 November 2006)
Bugs fixed:
- Fixed issue where users upgrading were not able to access a new Pro version trial.
Version 2.0 (2 August 2006)
Features added:
- New visual style and icons
- Agent interface improved
- Search interface improved
- Improved local sequence similarity search
- Additional import formats: PileUp, DNA Strider, Rich Sequence Format
- Import *.ab1 and other chromatogram files
Features added in Pro version:
- Collaboration (beta)
- Sequence editing
- Alignment editing
- ClustalW alignment
- Chromatogram viewer including sequence logos
- Open reading frame (ORF) finder
- Alignment via profile of Alignment and Sequence or two alignments
- New sequence creation
- Phylogeny tree display in Alignment View.
- Consensus sequence in Sequence View.
Bugs fixed:
- Alignment using excessive memory
Version 2.0.10 (4 October 2006)
Bugs fixed:
- fixed crash when exporting chromatograms
- fixed nexus tree importing bug.
Version 2.0.6 (07 September 2006)
Bugs fixed:
- fixed crash when dealing with chromatograms with no quality information
- fixed failure to import some abi (chromatogram) files.
- fixed fasta importing bug where all sequences that shared the same name would all receive the same description
- could not start up Geneiuos if the data location is invalid (drive letter changed/network drive etc.)
Version 2.0.5 (24 August 2006)
Bugs fixed:
- crash on startup after enabling direct connect option in preferences.
- Tree View significant figures option now works for consensus.
- occasional crash on startup when loading the contents of a folder.
Version 2.0.4 (14 August 2006)
Features added:
- Support for authenticated proxy servers
Bugs fixed:
- Crashes involving chromatogram documents
- Agents retrieving documents multiple times
Version 1.2 (31 May 2006)
Features added:
- Generate consensus sequence
- Fast alignment option
- Auto detection of FASTA sequence type
- Endnote 9.0xml file support
Bugs fixed:
- Database stability improved
- Database memory leak
Patch 1.2.1 (21 June 2006)
Bugs fixed:
- documents imported from Nexus and Clustal files in 1.0 crashing in 1.2