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Contents
1
Getting Started
1.1
Downloading & Installing Geneious Prime
1.2
Geneious Prime setup
1.2.1
User preferences
1.2.2
Choosing where to store your data
1.2.3
Sharing files or the local database
1.2.4
Changing the memory available to Geneious Prime
1.2.5
Connecting to the internet from within Geneious Prime
1.2.6
Installing plugins and customizing features
1.3
Upgrading to new versions
1.3.1
Downgrading to an earlier version
1.3.2
File compatibility
1.4
Licensing
1.4.1
Activate License
1.4.2
Install FLEXnet
1.4.3
Borrow Floating License
1.4.4
Release License
1.4.5
Buy Online
1.5
Troubleshooting
2
The Geneious Prime Main Window
2.1
The Sources Panel
2.2
The Document Table
2.3
The Document Viewer Panel
2.3.1
General viewer controls
2.4
The Toolbar
2.4.1
Status bar
2.5
The Help Panel
2.6
Geneious Prime menu bar options
2.6.1
File Menu
2.6.2
Edit Menu
2.6.3
View Menu
2.6.4
Tools Menu
2.6.5
Sequence Menu
2.6.6
Annotate & Predict Menu
2.6.7
Help Menu
3
Importing and Exporting Data
3.1
Importing data from the hard drive to your Local folders
3.1.1
Bulk import of multiple files
3.2
Data input formats
3.3
Importing files from public databases
3.3.1
UniProt
3.3.2
NCBI (Entrez) databases
3.3.3
Literature searching
3.4
Agents
3.4.1
Creating agents
3.4.2
Checking agents
3.4.3
Manipulating an agent
3.5
Exporting files
3.5.1
Export to comma-separated (CSV) or tab-separated (TSV) files
3.5.2
Exporting multiple files
3.5.3
Drag to desktop Genbank export
3.6
Printing and Saving Images
3.6.1
Printing
3.6.2
Saving Images
4
Managing Your Local Documents
4.1
Organizing your local documents
4.1.1
Moving files around
4.1.2
Aliases
4.1.3
Deleting Data and the Deleted Items folder
4.1.4
Adding note documents to folders
4.1.5
Searching folders
4.1.6
Calculating folder size on disk
4.2
Searching and filtering local documents
4.2.1
Advanced Search options
4.2.2
Similarity (“BLAST-like”) searching
4.2.3
Find in Document
4.2.4
Filtering and Similarity sorting
4.3
Find Duplicates
4.4
Batch Rename
4.5
Backing up your local documents
4.5.1
Restoring a backup
4.6
Document History
5
Creating, Viewing and Editing Sequences
5.1
Creating new sequences
5.1.1
Sequence lists
5.2
The Sequence Viewer
5.2.1
Zoom level
5.2.2
Selecting part of a sequence
5.2.3
Circular sequences
5.2.4
Genome View
5.2.5
The Side Panel Controls
5.2.6
Sequence Colors
5.2.7
Graphs
5.2.8
Advanced sequence view options
5.2.9
Statistics
5.3
Editing sequences
5.3.1
Concatenating sequences
5.4
Complement and Reverse Complement
5.5
Translating sequences
5.5.1
Genetic Codes
5.5.2
Back Translating
5.6
Viewing chromatograms
5.6.1
Binning by quality
5.7
Meta-data
5.7.1
Adding meta-data
5.7.2
Editing Meta-Data
5.7.3
Creating a new Meta-Data type
5.7.4
Editing Meta-Data Types
5.7.5
Using Meta-Data
6
Parent / Descendant Tracking
6.1
Editing Linked Documents
6.2
The Lineage View
7
RNA, DNA and Protein Structure Viewer
7.1
RNA/DNA secondary structure fold viewer
7.2
3D protein structure viewer
7.2.1
Structure View Manipulation
7.2.2
Selection Controls
7.2.3
Display Menu
8
Working with Annotations
8.1
Viewing, editing and extracting annotations
8.1.1
Viewing and Customizing Annotations: The Annotations and Tracks tab
8.1.2
The Annotations Table
8.1.3
Editing annotations
8.1.4
Extracting Annotations
8.2
Adding annotations
8.2.1
Manual creation of annotations
8.2.2
Importing annotations from external sources
8.2.3
Transferring annotations from other sequences
8.2.4
Annotation of sequence features using EMBOSS tools
8.3
Compare Annotations
9
Sequence Alignments
9.1
Dotplots
9.2
Sequence Alignments
9.2.1
Pairwise sequence alignments
9.2.2
Multiple sequence alignments
9.2.3
Sequence alignment using ClustalW
9.2.4
Sequence alignment using MUSCLE
9.2.5
Other sequence alignment plugins for Geneious Prime
9.2.6
Translation alignment
9.2.7
Combining alignments and adding sequences to alignments
9.3
Alignment viewing and editing
9.3.1
Highlighting
9.3.2
Alignment graphs
9.3.3
Concatenating alignments
9.4
Alignment masking
9.5
Consensus sequences
10
Assembly and Mapping
10.1
Supported sequencing platforms
10.2
Read processing
10.2.1
Setting paired reads
10.2.2
Trim Ends
10.2.3
Merging paired reads
10.2.4
Removing duplicate reads
10.2.5
Removing chimeric reads
10.2.6
Error correction and normalization of reads
10.2.7
Splitting multiplex/barcode data
10.3
De novo assembly
10.3.1
The de novo assembly algorithm
10.4
Map to reference
10.4.1
Choosing reference sequences
10.4.2
Fine tuning
10.4.3
Deletion, insertion and structural variant discovery (DNA mapping)
10.4.4
RNAseq mapping
10.4.5
The map to reference algorithm
10.5
Viewing Contigs
10.6
Editing Contigs
10.7
Extracting the Consensus
11
Analysis of Assemblies and Alignments
11.1
Finding polymorphisms
11.1.1
Find Variations/SNPs
11.2
Analyzing Expression Levels
11.2.1
Calculating Expression Levels
11.2.2
Comparing Expression Levels
11.2.3
Geneious Method for Comparing Expression Levels
11.2.4
DESeq2 Method for Comparing Expression Levels
11.2.5
Results
11.2.6
Principal Component Analysis for DESeq2 results
11.2.7
Volcano Plots
11.2.8
Comparing Expression Levels Using the DESeq2 Method on Linux Systems
12
Building Phylogenetic Trees
12.1
Phylogenetic tree representation
12.2
Tree building in Geneious Prime
12.2.1
Using alignment masks
12.3
Tree building methods and models
12.3.1
Neighbor-joining
12.3.2
UPGMA
12.3.3
Distance models or molecular evolution models for DNA sequences
12.3.4
Distance models or molecular evolution models for Amino Acid sequences
12.3.5
Advanced Tree Building methods
12.4
Resampling – Bootstrapping and jackknifing
12.4.1
Consensus trees
12.4.2
Creating a consensus tree of existing trees
12.4.3
Sort topologies
12.5
Viewing and formatting trees
12.5.1
Current Tree
12.5.2
General
12.5.3
Layout
12.5.4
Formatting
12.5.5
Show Tips, Node and Branch Labels
12.5.6
Automatically collapse subtrees
12.5.7
Show scale bar
12.5.8
Statistics
12.5.9
The Toolbar
13
Primers
13.1
Design New Primers
13.1.1
Generic primers
13.1.2
Cloning primers
13.1.3
T
m
calculation
13.1.4
Characteristics
13.1.5
Primer Picking Weights
13.1.6
Degenerate Primer Design
13.1.7
Advanced Options
13.1.8
Batch Primer Design
13.1.9
Output from Primer Design
13.1.10
When no primers can be found
13.2
Manual primer design
13.3
Importing primers from a spreadsheet
13.4
Primer Database
13.5
Test with Saved Primers
13.6
Add Primers to Sequence
13.7
Characteristics for Selection
13.8
Convert to Oligo
13.9
Primer Extensions
13.10
Extract PCR Product
13.11
More Information
14
Cloning
14.1
Find Restriction Sites
14.2
Digest into fragments
14.2.1
Direct extraction of restriction fragment
14.3
Creating a custom enzyme set
14.4
Introduction to the cloning interface
14.5
Restriction Cloning
14.6
Golden Gate
14.6.1
Sequence ordering, rules and assumptions
14.7
Gibson Assembly
14.8
Gateway
®
Cloning
14.9
TOPO
®
Cloning
14.10
Copy-paste cloning
14.11
CRISPR site finder
14.12
Analyze Silent Mutations
14.13
Optimize Codons
15
BLAST
15.1
Setting up a BLAST search
15.2
BLAST results
15.2.1
BLAST hit table
15.2.2
Query-centric view
15.3
NCBI BLAST
15.3.1
Edit BLAST Databases
15.4
Adding alternative BLAST server locations
15.5
Custom BLAST
15.5.1
Setting up the Custom BLAST files through Geneious Prime
15.5.2
Setting up the Custom BLAST files yourself
15.5.3
Adding Databases
15.5.4
Using Custom BLAST
16
Workflows
16.1
Managing Workflows
16.2
Creating and editing Workflows
16.2.1
Configuring options for Operation and Steps
16.2.2
Advanced document management
16.3
Custom code in Workflows
17
Geneious Education
17.1
Creating a tutorial
17.2
Answering a tutorial
18
Saving Operation Settings (Option Profiles)
19
Shared Databases
19.1
Using a Shared Database
19.1.1
Overview of Direct SQL Connection
19.1.2
Overview of Geneious Server Database
19.1.3
Connecting to a Shared Database
19.1.4
Removing a Shared Database
19.1.5
Storing Documents in a Shared Database
19.1.6
Backing up your shared database
19.2
Direct SQL Connection
19.2.1
Setting up a Direct SQL Connection Shared Database
19.2.2
Administration of Direct SQL Connection Shared Databases
19.3
Geneious Server Database
19.3.1
Setting up a Geneious Server Database
19.3.2
Administration of Geneious Server Databases
19.3.3
Backing up a Geneious Server Database
19.3.4
Audit Logging
20
Geneious Server
20.1
Introduction to Geneious Server
20.2
Accessing Geneious Server
20.3
Running jobs and retrieving results
20.4
Geneious Server enabled plugins
21
Advanced Administration
21.1
Default data location
21.2
Change default preferences
21.2.1
Change preferences within Geneious Prime
21.2.2
geneious.properties file
21.3
Specify license server location
21.4
Deleting built-in plugins
21.5
Max memory
21.6
Web Linking to Data in Geneious Prime
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