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Columns in snipre input file and calculating total sites

Hi, thanks so much for putting your code online. I'm currently trying to use SnIPRE to test for positive selection in recently diverged bacterial populations.

I haven't been able to find the definitions of the columns for the SnIPRE input file. Is the following correct?

  • "geneID" - self explanatory
  • "PR" - # of nonsynonymous polymorphisms
  • "FR" - # of nonsynonymous divergences
  • "PS" - # of synonymous polymorphisms
  • "FS" - # of synonymous divergences
  • "Tsil" - total # of synonymous sites
  • "Trepl" - total # of nonsynonymous sites
  • "nout" - # of outgroup sequences
  • "npop" - # of sequences in population

How do you typically calculate the total number of nonsynonymous and synonymous sites?\

Thanks for your time.

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