Hi helsk,

Synonymous and non-synonymous trees are difficult to decouple. You can infer a codon-based tree to include both. There are ad hoc approaches to separate synonymous and non-synonymous contributions, most commonly by looking at the evolution of 1st and 2nd codon positions in a codon (dN) as opposed to the 3rd position (dS). This is rather crude approximation in the maximum likelihood framework. Alternatively you can compute synonymous and non-synonymous pairwise distances (e.g. using the Nei Gojobori estimators) and build neighbor joining trees on them.

Why are you interested in separating the two contributions, if you don't mind my asking?

Sergei

Actually I got the dNdS.bf to work now. I think this will do it.

Thanks
/helsk