Hi Santiago, it is possible to extract the information for the root for the sankoff algorithm in the phangorn package (this is for discrete characters). I'll added a function called pace, which will do the job. Of course maximum parsimony will not provide unique solutions, but several characters can be tied for the best score. When you look at more nodes at the same time things become more complicated. If you need information about other nodes the simplest would be to re-root the tree, this ensures that you have all possible states of your ancestral sequences.
This function is part of phangorn package 0.99-6, which I just uploaded. It should appear in the next days on CRAN. The command is like pace(tree, data) or pace(tree, data, cost) where tree is an object of class phylo, data of class phyDat and cost is matrix. It returns a matrix which TRUE or FALSE depending whether the character is an ancestral states according to MP. Should work for all kind of phyDat objects, e.g. nucleotide, AA or USER defined data. Cheers, Klaus On Sun, Jan 24, 2010 at 5:32 AM, Santiago Claramunt <scla...@tigers.lsu.edu> wrote: > Hi all, > Does anybody know a function in R for performing maximum parsimony ancestral > reconstructions? > Best, > > Santiago > > > Santiago Claramunt > Museum of Natural Science, > 119 Foster Hall, > Louisiana State University, > Baton Rouge, LA70803 > scla...@tigers.lsu.edu > http://www.museum.lsu.edu/Claramunt/Home.html > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > 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 R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
