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]/
