gravatar for Mensur Dlakic

34 minutes ago by

USA

Muscle can do this. If you save your alignment in aligned FASTa (.afa) format, which is default, all sequence headers will be preserved. Assuming your starting file is protein.fas:

muscle -in protein.fas -out protein.afa

After that the alignment can be converted to Stockholm format using HMMer's esl-reformat utility:

esl-reformat stockholm protein.afa > protein.sto



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