I have done several analysis to find dN/dS ratio in six species.
I found one-to-one orthologs (by orthofinder)
I did codon-based alignments of the orthologs that produced .paml format alignments.
I did protein alignment of the orthologs.
Now I would like to have your advice on:
How to concanate all paml files that are used in codeml.?
To be used in codeml (as tree file) do I need to perform phylogenetic of those .paml files? or it is fine to use all.paml files only in codeml?