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different output format in Clustal-Omega

in Clustal-Omega you can specify the output format for the alignment with the option --outfmt:

--outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} 
  MSA output file format (default: fasta)

I would like to have more than one of these output files. do you know if you can do it in one go? it would be quite unfortunate to have to run the program many times just to have a different output.

bash clustal
• 9,398 views • link
updated by Ram Ram • written by Martombo Martombo

1 answer

Hi Martombo,

you can't generate multiple output files with different format simultaneously in Clustal Omega (or any other alignment program I know of). Running Clustal for each format doesn't make sense though. It would be best to pick one and then reformat using your tools of choice, e.g. sreformat.

Andreas

• 3 views • link
updated by Ram Ram • written by Andreas Andreas

Many tools are available for reformatting alignments, for example:

In addition most alignment editor/viewers can reformat alignments (see http://en.wikipedia.org/wiki/List_of_alignment_visualization_software).

FWIW there are some multiple sequence alignment programs that can produce multiple output formats per run, for example T-COFFEE produces multiple formats by default.

As the OP mentions supporting multiple output formats per run, is a useful feature and something I have requested for Clustal Omega in the past. I suggest any users who want to see the feature in a future version of Clustal Omega register their interest by letting the Clustal developers know by sending a request to clustalw@ucd.ie (see http://www.clustal.org/omega/#Contact).

• 3 views • link
updated by Ram Ram • written by hpmcwill hpmcwill

yes exactly, I was comparing t-coffee to clustal-omega and I was wondering if you could get the same multiple output. I'll send this request to the developers.

• 2 views • link
written by Martombo Martombo

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