Estimating synonymous substitution rate

Question

[cbaudo]

Hello,

I'd like to estimate the synonymous substitution rate for genes within a single copy region and within an inverted repeat (similar to this article: http://onlinelibrary.wiley.com/doi/10.1111/nph.13743/full). I'm working on several species within a single genus and wonder how I should go about doing this. As I understand it, most synonymous substitution rate estimators take an input of a pair of sequences. Is there any way I could calculate the substitution rate across all species or do I have to artificially select pairwise comparisons?

Thank you, Charles

Answer 1

[hbw]

Use paml and maybe infer a hypothetical ancestral sequence to calculate the substitution rates against. Think about which rate you actually want. Substitution since the most recent ancestor? Then you should organize the species in a phylogenetic tree.