I have a question about the method used in the PAML program (Yang, Z.
1996. Phylogenetic Analysis by maximum likelihood (PAML) Version 1.2.
Department of Integrative Biology, University of California at Berkeley.)
to determine the number of synonymous substitution sper synonymous site to
the number of nonsynonymous substitutions per nonsynonymous site and the
ratio, if anyone could help. In section 5.2.1 of the documentation, it is
stated that the method of Nei and Gojobori is used to calculate these, but
then in the next paragraph it is stated that they are calculated by the
codon-based model following Goldman and Yang. Having read both papers and
the documentation for PAML, I am now unclear as to which method is
actually used (this is using codonml). Later in section 6.2 it states
that it is the Goldman and Yang method that is used if the option runmode=
-2 (but then I get an error method after 4 or 5 pairwise comparisons).
Can anyone help me or give me guidance as to when and how these two
methods are used in PAML. I would appreciate any help at all..