Hello all,

I have conducted branch-site analyses to identify positively selected codons on specified branches using PAML.

In contrast to PAML, using branch-specific analyses of codon selection pressures in HYPHY, I regularly find non-signficicant results when applying non-synonymous rate heterogeneity.

Has anyone had similar experiences and, if so, is this logical? I think this finding is unlikely to be widespread if different codon positions are involved in positive selection on an amino acid. Still, many of the codons in the genes I examined are not variable in only one of the three codon positions.

Any ideas on this?

Thanks, Yer