How to calculate rate of synonymous substitution at 4 fold and 2 fold degenerate sites?
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2.5 years ago

Hello experts,

'Bierne, Nicolas, and Adam Eyre-Walker. "The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias." Genetics 165.3 (2003): 1587-1597.' https://www.ncbi.nlm.nih.gov/pubmed/14668405

However, I want to know how can I calculate the rate of synonymous substitution at four-fold (DTs4) , rate synonymous substitution at two-fold degenerate sites (dBs2) and the total number of synonymous substitutions per codon (DcBs) . How can I calculate it is there any software available for the same. HELP

gene substitution PAML • 875 views