ka/ks for comparing more than 2 protein sequences
Does it make sense to calculate ka/ks comparing more than 2 species (so not comparing just pair of orthologs) to study protein evolution and identify patterns of selection??
If yes, what do you think it is the limit to correctly analyze ka/ks mantaining a reasonable distribution? I’ve been encountering studies which do this within species with 3+ up to 10 accessions, but I know it is best to do it pairwise so I’m a bit confused on this.
If no, what alternative would you recommend to analyze genetic diversity for a specific gene family in an entire population for that species (or closely related, say >200 individuals) at the gene level.
Thanks for any help
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