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Export alignments in Nexus format (Read 4164 times)
Mar 16th, 2013 at 3:56pm

Peter   Offline
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At the moment, the allowable formats to export alignments from UGENE are: FASTA, FASTQ, GFF and Genbank.

Nexus is a standard format for alignments as input into lots of phylogenetic programs

Therefore it would be great if UGENE allowed the export of alignments in Nexus format.

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Reply #1 - Mar 18th, 2013 at 1:12pm

Yuriy Vaskin   Offline
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Posts: 138

thank you for your suggestion. As far as I understand you tried to export alignment to sequence format using Export->Expoert alignment to sequence format. This will create a file with multiple sequences in it, but not an alignment file.

To create another alignment file try to open the context menu of the Document and select "Export Document".

This is not obvious, so, we are going to add(https://ugene.unipro.ru/tracker/browse/UGENE-1520) this option into "Export" menu you opened at the first place.
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Reply #2 - Apr 8th, 2015 at 2:44pm

Olga Golosova   Offline
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Posts: 222
In UGENE 1.16.1 to export an alignment to the NEXUS format:
1) Select "Export/Import > Export object"
2) Select "NEXUS" in the appeared dialog and click "OK".
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