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!

Hi JKN, sorry to have steered you in the wrong direction to start with and thanks for coming back to get the right answer recorded.