Is there an R package that computes homoplasy excess ratios (HER)? 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 &quot;homoplasy excess ratio&quot; 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.