<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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2020-11-13T11:31:47.040Z
2020-11-13T11:31:47.040Z
M__
<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>

<r><phylogenetics><phylogeny><covid-19><sars-cov-2>
Is there an R package that computes homoplasy excess ratios (HER)?
# 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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