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How to specify codon based multiple sequence alignment in clustalw command line?

I need to carryout multiple sequence alignment using clustalw command line. I have been using the following command line which works fine. clustalw -infile=test.fasta -align -type=DNA -score=PERCENT -outfile=clus_test -output=FASTA In addition, I need to specify codon base alignment in the command line. Please help me to do the same.

Many thanks in advance.

clustalw fasta alignment sequence gene
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updated by lieven.sterck lieven.sterck • written by Kumar Kumar

CLUSTAL (any of the variants, as far as I know) cannot do codon-aware alignments, as Lieven pointed out.

In addition to his suggestion, I think you can use CodonW and PAML for this.

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written by Joe Joe

1 answer

I don't think you can do that with clustalw.

You could perhaps try tools such as Pal2Nal or PRANK? There will also be some custom PERL or python implementation for this I suppose.

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written by lieven.sterck lieven.sterck

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