Implementing McDonald-Kreitman test

Question

[GR]

Dear All,

I am writing a python script to implement McDonald-Kreitman test. I am not sure how to deal with the case of multiple mutations per codon. I have a population data from 50 individuals. Can someone help me with this.

Thanks. RT

Answer 1

[mt1022]

I met the same problem recently and I assign assign equal weight to all possible mutation path. For example, for TTC to CTA, TTC->TTA->CTA and TTC->CTC->CTA have the same probability, as I am dealing triplet change in noncoding region. The following article talks more sophiscated method for this problem:

Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models http://mbe.oxfordjournals.org/content/17/1/32.full

[GR]

I end up using python egglib library for this...