Question: Estimating synonymous substitution rate
gravatar for cbaudo
4.7 years ago by
cbaudo10 wrote:


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: 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

ADD COMMENTlink modified 4.6 years ago by hbw80 • written 4.7 years ago by cbaudo10
gravatar for hbw
4.6 years ago by
United States
hbw80 wrote:

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.

ADD COMMENTlink written 4.6 years ago by hbw80
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