Dear Albert,

You can use the steps outlined in [url]http://www.hyphy.org/cgi-bin/yabb/YaBB.pl?board=How2;action=display;num=1101838973;start=3#3[/url] 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