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.

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.

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

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.