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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?

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.

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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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