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