Matthew- In addition to Ross's suggestion of TNT, I would recommend that you consider options less commonly used by paleontologists. One option is Mr. Bayes, which can apply the Mk2 model from Lewis (2001) to morphological data. Another is Strataphy (Marcot and Fox, 2008) which can apply stratocladistics (if you are willing to work with the assumptions of that method; I realize some people have strong opinions against it). Note that both these methods require that autapomorphies are included. -Dave Bapst, UChicago
On Mon, Mar 28, 2011 at 12:34 AM, Matthew Vavrek <matt...@matthewvavrek.com>wrote: > Hello, > although I know a lot of people have moved away from it, I was wondering if > there is an implementation of a tree search function using maximum parsimony > with a branch and bound option for R. I work in a lab that has been using > PAUP forever, but I'm trying to see if R would be a viable alternative > (especially since PAUP seems to be in some sort of limbo, from what I can > gather on the intertubes). However, maximum parsimony is typically what is > used, and usually the datasets that were being used could be run in a > relatively short (ie 15 minutes) time span in PAUP using a branch-and-bound > search, thereby locating all the most parsimonious trees. I've tried the > phangorn package which has a parsimony ratchet function that works really > well, but within paleontology (my field) there are still a good number of > people that want an exhaustive search. Alternatively, if there is no > exhaustive search, what would be the best tree search function for > morphological (character) data? Most of the discussions I can find revolve > more around DNA/molecular data, which are hard to come by in fossils (unless > you are Michael Crichton). > > Thanks > Matthew Vavrek > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
