Hello all, Another implementation of RF distances and others that I found easy to use is:
Bogdanowicz, D., Giaro, K., & Wróbel, B. (2012). TreeCmp: Comparison of trees in polynomial time. Evolutionary Bioinformatics Online, 8, 475. Best, Eduardo On Apr 14, 2014, at 1:30 PM, Eduardo Ascarrunz <[email protected]> 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 <[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]/ [[alternative HTML version deleted]]
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