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/
