I have a nucleotide alignment that I would want to calculate dn/ds ratios for the 1st, 2nd and 3rd codon positions separately. I would like to know if there is a tool to perform this analysis.

I extracted the codon positions from the nucleotide alignment using DNAsp and saved it in nexus format but when I upload into datamonkey, I get an error message saying my sequence has stop codons. It seems like datamonkey is reading the file as codons instead of individual codon positions. Is there a functionality for datamonkey or any tool to read codon positions from a nucleotide alignment and perform dn/ds ratio analysis on each codon position?

I need help. Thanks.

Hi there,

dN/dS is defined for codon data  -- you cannot calculate it for individual codon positions [perhaps you were thinking of something like the SRD06 model in BEAST? Those would be nucleotide rates]. Please take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login to review how dN/dS calculations work.

Sergei