Dears,

I would like to know if it is possible to have the values of S and N,
and S*dS and N*dN in each branch for the Local/Free-Ratios models of
codon evolution.

I'm trying to compare the dN and dS values in each of the branches,
with given parameters, with respect of these values of S,N in the tree
(and S*dS,N*dN in each branch).

Thanks in advance,

Bests,

   Albert.

Dear Albert,

You can use the steps outlined in Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login to obtain the expected numbers of synonymous and non-synonymous substitutions per (nucleotide) site along every branch.

I am not entirely certain how PAML computes S,N and ds*S, dN*N (if these are indeed the quantities you are interested in). I skimmed the documentation for PAML, and the details don't seem to be there. If you can point me to a reference where the quantities are defined, I'll be happy to tell you how they can be evaluated.

Cheers,
Sergei