Hello again, Here are the programs.
*HashRF* by Sul & Williams - You will need a Unix console for using this, or cygwin if you only run Windows https://code.google.com/p/hashrf/ *FastRF* by Pettengale et al. - The download link seems to be broken! You'll probably have to contact the authors. http://agl.cs.unm.edu/~moret/recomb_jcb06.pdf http://lcbb.epfl.ch/phylo0/Nick_Pattengale.html *Trex server*, with an implementation of Makarenkov & Leclerc's (2000) method http://www.trex.uqam.ca/index.php?action=rf&project=trex Hopefully you'll get what you need with one of those. Best, E. On 14 April 2014 14:57, Eduardo Ascarrunz <[email protected]> wrote: > Hello Chris, > > I know there's a program that was specifically developed for calculating > large pairwise Robinson-Foulds distances matrices efficiently. I'll be able > to send you the reference this evening (Paris time). > > All the best, > > E. > On 14 Apr 2014 14:44, "Chris Buddenhagen" <[email protected]> wrote: > >> Thanks. That answers part of the question. It isn't the comparison of any >> single pair of topologies that is troubling, but a quick means of doing >> all >> the possible comparisons between 100s of loci. >> >> Chris Buddenhagen >> Florida State University >> [email protected] >> >> >> On Mon, Apr 14, 2014 at 8:27 AM, Mattia Prosperi <[email protected]> >> wrote: >> >> > You may use "dist.topo" from the ape package, there are a couple of tree >> > distance functions implemented. >> > >> > >> > 2014-04-14 13:13 GMT+01:00 Chris Buddenhagen <[email protected]>: >> > >> >> I would like to make pairwise comparisons of topological similarity >> >> between >> >> all possible combinations of 518 gene trees. >> >> >> >> The expected output would be a matrix of topological distances for each >> >> gene tree to each other tree. >> >> >> >> Any suggestions? >> >> >> >> Also as an aside, is there a way to mechanize the estimation of 100s of >> >> gene trees from alignments, such that the best model models of >> nucleotide >> >> substitution is chosen objectively and then a tree is generated using >> >> likelihood or Bayesian methods. Ideally I give the program the folder >> of >> >> 100s of alignments and tell it to go and wait for the gene trees. >> >> >> >> Best >> >> Chris Buddenhagen >> >> Florida State University >> >> [email protected] >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> >> R-sig-phylo mailing list - [email protected] >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> >> Searchable archive at >> >> http://www.mail-archive.com/[email protected]/ >> >> >> > >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at >> http://www.mail-archive.com/[email protected]/ >> > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
