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.
|Data type||Export format options|
|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|
|Document Properties||CSV, TSV, Geneious|
|Text ﬁles||.txt, CSV, TSV, Geneious|
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.