text: user2961: I want to calculate the homoplasy excess ratio for a phylogenetic tree, for example homoplasy resulting from recombination.
  I am wondering if there are any R packages out there that will do this?
  I have looked at phyloseq, Rphylopars, phylocurve, PhylogeneticEM, PhyloinformR, but these packages do not have functions that calculate HER. I searched "homoplasy excess ratio" on bioconductor, but it returned ca. 3000 packages.
  
  user3848: Maynard's Smith's homoplasy is what you want and it is available in the recombination detection package (RDP) described here. Its really a Windows package rather than R.
  
original_text: 2961: <p>I want to calculate the homoplasy excess ratio for a phylogenetic tree, for example homoplasy resulting from recombination.</p>
  <p>I am wondering if there are any R packages out there that will do this?</p>
  <p>I have looked at phyloseq, Rphylopars, phylocurve, PhylogeneticEM, PhyloinformR, but these packages do not have functions that calculate HER. I searched &quot;homoplasy excess ratio&quot; on bioconductor, but it returned ca. 3000 packages.</p>
   3848: <p>Maynard's Smith's homoplasy is what you want and it is available in the recombination detection package (RDP) described <a href="https://academic.oup.com/ve/article/1/1/vev003/2568683" rel="nofollow noreferrer">here</a>. Its really a Windows package rather than R.</p>
  