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??