UGENE Forum
http://ugene.net/forum/YaBB.pl
General Category >> Bugs and Issues >> mafft aligner via cmd line
http://ugene.net/forum/YaBB.pl?num=1499177317

Message started by adam54546 on Jul 4th, 2017 at 9:08pm

Title: mafft aligner via cmd line
Post by adam54546 on Jul 4th, 2017 at 9:08pm
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.

Title: Re: mafft aligner via cmd line
Post by Olga Golosova on Jul 6th, 2017 at 7:56pm
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 | 162 )

Title: Re: mafft aligner via cmd line
Post by Reedmans on Mar 30th, 2019 at 6:28pm
Is it possible to run multiple workflows at the same time in the command line?

Title: Re: mafft aligner via cmd line
Post by Olga Golosova on Apr 1st, 2019 at 11:04am

Quote:
Is it possible to run multiple workflows at the same time in the command line?

Hi! What do you mean by "at the same time"?

You can run any workflow from the command line if you configure the command line aliases properly (see https://ugene.net/wiki/display/WDD32/Running+Workflow+from+the+Command+Line).
And you can run several commands one by one in the command line ("Terminal") windows.

I.e. workflows can be executed simultaneously, the commands that run the workflows will be input one after another.

UGENE Forum » Powered by YaBB 2.5 AE!
YaBB Forum Software © 2000-2010. All Rights Reserved.