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]/
