Regarding finding all most parsimonious trees by branch-and-bound: Program Penny in my PHYLIP package could be called from within R, driven by batch scripts. You'd have to make them yourself, but it's not hard. However Penny can handle only 0/1 characters, and if there is a multifurcation it will return all the binary trees compatible with that. It is also much slower than PAUP*.
It would get you a file of Newick trees. Joe ---- Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
