To export files from Geneious Prime, select the file or files you want to export and click File → Export → Selected Documents. Each data type has several export options, as detailed in the table below. Any set of documents may be exported in Geneious native format, and these files are back-compatible to Geneious version 6.0 (e.g. Files exported in .geneious format from Geneious R7 and above can be imported to Geneious R6 or later).
If you wish to export the parents and/or descendants of a particular file at the same time, choose File → Export → with Parents/Descendants.
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Data type | Export format options |
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DNA sequence | FASTA, Genbank (XML or flat), CSV/TSV, Geneious |
Amino acid sequence | FASTA, Genbank (XML or flat), CSV/TSV, Geneious |
Chromatogram sequence | ABI, Geneious |
Sequence with quality | As above, also FastQ, Qual |
Annotation | GFF, BED, Genbank, Geneious |
Alignment or Assembly | Phylip, FASTA, NEXUS, MEGA, Phrap ACE, SAM/BAM, Geneious |
Variant calls | VCF (single sample only) |
Phylogenetic tree | Phylip, FASTA, NEXUS, Newick, MEGA, Geneious |
PDF document | PDF, Geneious |
Publication | EndNote 8.0, Geneious |
Graphs | CSV, WIG |
Document Properties | CSV, TSV, Geneious |
Text files | .txt, CSV, TSV, Geneious |
Assembly report | .html |
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Documents imported in any chromatogram or molecular structure format can be re-exported in that format as long as no changes have been made to the document.
Both fasta and fastq files can be exported in compressed (fasta.gz and fastq.gz) format for smaller file size. If exporting paired reads in fasta format, an option to export the forward and reverse reads to separate files is available by choosing ’Fasta Paired Files’ as the file type option.