Using Rate4Site To Calculate Mutation Rate Per Gene?

Question

[anin.gregory]

I would like to calculate the mutation rate per gene based on an MSA. In this past post (C: Mutation rates for a specific gene?) someone suggested using Rate4Site to calculate mutation rate per gene. However the program is specifically designed to calculate the conservation score for each amino acid, with a lower value indicating higher conservation.

I read the associated papers Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues and Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior, and I don't understand how you can get from the conservation score to a mutation rate. Maybe I am missing something in the papers. Has anyone tried using Rate4Site to calculate mutation rate per amino acid / per gene??

Answer 1

[Asaf]

The rate of each position (the r parameter which is the only parameter estimated) appears in the output sent to stdout or to a file using the option -y filename. The conservation scores are just z-scores of these rates, normalized for each gene.

[anin.gregory]

I'm sorry. I still don't understand how this is the mutation rate. It is saying that the rate is 0.9999. This does not make sense, since mutation rates are usually in 10^-8 orders of magnitude for my system. Am I doing something wrong? I an MSA and use the default NJ tree option. Thanks in advance.