Trimming Codon Alignments For Phylogenetic Analysis

Question

[Pappu]

I want to remove the non-conserved regions and sequences >90% identical from the codon alignment obtained from pal2nal. Thus I would like to reduce the complexity prior to phylogenetic tree construction and fitting evolutionary models using codeml. Could you suggest a tool for that?

Answer 1

[Biojl]

For removing non-conserved regions a great tool is Trimal

If you want to use CodeML is a bad idea to remove sequences >90% identical because you will be losing precisely the interesting regions where changes occur. We discuss some of this in our paper.

[Pappu]

I did not see any optiono of trimming codon alignment in trimal. I am comparing >100 sequence tree using codeml and it does not converge.

[Biojl]

No, there is not such an option. You can either trim protein alignments and then convert them back or talk to the developer.