Hi all, the package PHYLOCH from Christoph Heibl seems to do exactly what Joe Felsenstein suggested, calling Penny from within R. The homepage is http://www.christophheibl.de/Rpackages.html
Regards, Klaus On 3/28/11, Joe Felsenstein <[email protected]> wrote: > > 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 [email protected] > Department of Genome Sciences and Department of Biology, > University of Washington, Box 355065, Seattle, WA 98195-5065 USA > > _______________________________________________ > R-sig-phylo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
