I was just looking for some clarification on the meaning of the dn and ds outputs from a pairwise comparison in codeml of PAML.
Is dn the rate of non-synonymous subs per non-synonymous site? Or is it per codon?
Given they are rates, what is the unit of time? From reading the literature, I get the impression that the transfer matrix is normalised in such a way that the 'rate' is then the actual expected number of substitutions between the two sequences (per site type). Is this correct?
Further to this, if ds > 1 for a pairwise comparison, does this imply that all synonymous sites have expected to have been substituted?
Thanks for any help!