Answers.Body: <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>
  
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Body: <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>
  
Tags: <r><phylogenetics><phylogeny><covid-19><sars-cov-2>
Title: Is there an R package that computes homoplasy excess ratios (HER)?
ThreadText: # Is there an R package that computes homoplasy excess ratios (HER)?
  
  (Asked by: username_0 on 2018-10-24)
  
  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.
  
  **Tags:** r, phylogenetics, phylogeny, covid-19, sars-cov-2
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2020-11-13. Score: 1
  
  Maynard's Smith's homoplasy is what you want and it is available in the recombination detection package (RDP) described [here](https://academic.oup.com/ve/article/1/1/vev003/2568683). Its really a Windows package rather than R.
  
  
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