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I am investigating the rate of synonymous non synonymous substitutions and would like to find the Ka/Ks value also known as dn and ds between multiple alleles? I want to investigate multiple alleles because I am examining the MHC region which is highly polymorphic. Any suggestions would be very helpful!

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I have also used the seqinr package for Ka/Ks

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A while back, I used PAML for this purpose for a phylogenetics project. It has Windows and macOS executables but for *nix, you will need to compile it from source code.

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