---------- Forwarded message ---------- From: Klaus Schliep <klaus.schl...@gmail.com> Date: Thu, Aug 22, 2013 at 6:12 PM Subject: Re: [R-sig-phylo] Collapsing branches with low bootstrap values To: "Naxerova, Kamila" <naxer...@fas.harvard.edu>
Hi Kamila, try function pruneTree in phangorn. data(woodmouse) f <- function(x) nj(dist.dna(x)) tr <- f(woodmouse) X = boot.phylo(tr, woodmouse, f, trees = TRUE) tree = plotBS(tr, X$trees) tree2 = pruneTree(tree, 75) par(mfrow=c(2,1)) plot(tree, show.node=TRUE) plot(tree2, show.node=TRUE) Cheers, Klaus On Thu, Aug 22, 2013 at 5:09 PM, Naxerova, Kamila <naxer...@fas.harvard.edu>wrote: > Dear list, > > is there a function that will take a tree and the output of boot.phylo() > and collapse branches below a chosen bootstrap value cutoff? > > Many thanks. > Kamila > > _______________________________________________ > 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/ > -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http://darwin.uvigo.es/kschliep/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http://darwin.uvigo.es/kschliep/ [[alternative HTML version deleted]] _______________________________________________ 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/
