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

Question

[Kumar]

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.

[Joe]

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.

Answer 1

[lieven.sterck]

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.