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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.
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.
