Does PAML (codeml ) analysis include the introns or it correspond only to the CDS ?

Question

[Michel Edwar]

I have done a phylogeny tree using protein sequences. Now I want to measure dn/ds on several branches. If I want to work on the nucleotide level, can I do the analysis using the corresponding coding region only or do I need to include the introns as well?

Answer 1

[h.mon]

codeml models codon (if input is DNA) or amino acid (if input is peptides) substitution, so yes, you should use only the coding part of your sequences.

[Brice Sarver]

Building on this, you can't just give it -any- coding sequence. It needs to be in the appropriate frame or the analysis is meaningless.