Hi

I was wondering how i can infer a dN and adS ML tree respectively from one codon aligned sequence alignmnet.

Best
/helsk

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

I'm looking at pol sequences of HIV-1. There are drug resistance mutations in some of my sequences. I want to see if these sequences still are clustering if I look at synonymous sites as compared to non-synonymous sites. So therefor I want to dived my codon alignment in two you might say. One for synonymous sites and one for non-synonymous sites. I could do this by only looking at 3rd codon position versus 1+2 codon position trees but I was wondering if there is a better way to do this.

Cheers

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

Thanks
/helsk