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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?

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  • $\begingroup$ Did you try phyloseq, or other Bioconductor packages related to phylogenetic trees? A search returned packages from CRAN: Rphylopars, phylocurve, PhylogeneticEM, PhyloinformR, but I couldn't read if they have datasets or not $\endgroup$ – llrs Oct 25 '18 at 7:33
  • $\begingroup$ These packages do not have functions that calculate HER. I searched "homoplasy excess ratio" on bioconductor, but it returned ca. 3000 packages. $\endgroup$ – Namenlos Oct 25 '18 at 19:52
  • $\begingroup$ The homoplasy index should be derived from the RDP package. It would be quite easy to write it, its Maynard-Smiths old calculation. $\endgroup$ – M__ Dec 28 '18 at 21:20
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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.

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