text: user12135: 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!
  
  user3541: 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.
  
  user12660: I have also used the seqinr package for Ka/Ks
  
original_text: 12135: <p>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!</p>
   3541: <p>A while back, I used <a href="http://abacus.gene.ucl.ac.uk/software/paml.html" rel="nofollow noreferrer"><code>PAML</code></a> 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.</p>
   12660: <p>I have also used the <a href="https://cran.r-project.org/web/packages/seqinr/index.html" rel="nofollow noreferrer">seqinr</a> package for <a href="https://www.rdocumentation.org/packages/seqinr/versions/4.2-8/topics/kaks" rel="nofollow noreferrer">Ka/Ks</a></p>
  