Thanks everyone who has helped. Chris Buddenhagen Florida State University cbuddenha...@gmail.com
On Mon, Apr 14, 2014 at 1:30 PM, Eduardo Ascarrunz <ear...@gmail.com> wrote: > 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 <ear...@gmail.com> 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" <cbuddenha...@gmail.com> 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 >>> cbuddenha...@gmail.com >>> >>> >>> On Mon, Apr 14, 2014 at 8:27 AM, Mattia Prosperi <ahn...@gmail.com> >>> 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 <cbuddenha...@gmail.com>: >>> > >>> >> 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 >>> >> cbuddenha...@gmail.com >>> >> >>> >> [[alternative HTML version deleted]] >>> >> >>> >> _______________________________________________ >>> >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> >> Searchable archive at >>> >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >>> >> >>> > >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> Searchable archive at >>> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >>> >> > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
