Karla Shikev -- > I just want to take a tree with node labels (e.g. > bootstrap values from a RAxML analysis) and collapse all nodes with support > values below, say, 90%.
People here have given you various ways of doing this in R. I am not very familiar with the R packages, but just wanted to add one more way. If you have the original set of trees that were used to get the bootstrap values, you can do a version of the bootstrap that makes a tree which shows only the groups that are present in 90% or more of the input trees. This is called an M(0.90) consensus tree (the 0.90 is in a subscript which I can't typeset in an email). It is available in the program Consense in my PHYLIP package, and also in some other phylogeny packages. If you prefer R you can use Liam Revell's Rphylip package, together with installing a copy of PHYLIP, as Rphylip serves as a front-end for PHYLIP within R. J.F. ----- 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 Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
