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mafft aligner via cmd line (Read 975 times)
Jul 4th, 2017 at 9:08pm

adam54546   Offline
YaBB Newbies

Posts: 1
I'm having trouble using the mafft aligner via cmd line on windows. Essentially, it is working and aligning fine, but I want to know the different output formats I can set "--format=" to. Right now I know I can set "--format=" to "clustal" and "fasta", but I want to know what else I can set "--format=" to.
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Reply #1 - Jul 6th, 2017 at 7:56pm

Olga Golosova   Offline
YaBB Administrator

Posts: 265
In short, the formats are the following:
* clustal
* fasta
* mega
* msf
* nexus
* phylip-interleaved
* phylip-sequential
* stockholm

Under the hood the commands in the UGENE CLI are workflows of the UGENE Workflow Designer. Theey are actually stored in the "/data/cmdline" subfolder of the UGENE installation folder. If you open the "align-mafft.uwl" file in the Workflow Designer, you can see the available formats in the Property Editor (see the screenshot).

Note that you may run any workflow in the command line, if required.

formats.png (22 KB | 84 )
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