Thank you Klaus, this works like a charm. One more if I may: If I still want to have bootstrap values in my plot, how do I go about plotting those for my new tree?
Kamila On Aug 22, 2013, at 12:12 PM, Klaus Schliep <[email protected]<mailto:[email protected]>> wrote: 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 <[email protected]<mailto:[email protected]>> 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 - [email protected]<mailto:[email protected]> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http://darwin.uvigo.es/kschliep/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
