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?

  • $\begingroup$ 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

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.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.