Answers.Body: <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>
  
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Answers.Body: <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>
  
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Body: <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>
  
Tags: <r><snp><bash>
Title: Is there a way to calculate the Ka/Ks value in R/unix?
ThreadText: # Is there a way to calculate the Ka/Ks value in R/unix?
  
  (Asked by: username_0 on 2021-06-28)
  
  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!
  
  **Tags:** r, snp, bash
  
  
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  ## 2 answers
  
  ### Answer by username_1 on 2021-06-30. Score: 2 | Accepted answer
  
  I have also used the [seqinr](https://cran.r-project.org/web/packages/seqinr/index.html) package for [Ka/Ks](https://www.rdocumentation.org/packages/seqinr/versions/4.2-8/topics/kaks)
  
  
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  ### Answer by username_2 on 2021-06-29. Score: 1
  
  A while back, I used [`PAML`](http://abacus.gene.ucl.ac.uk/software/paml.html) 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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