Dear Klaus, Thanks a lot for your kind reply. That is really valuable for me.
Best wishes, Jian-Feng, 2012/8/7 Klaus Schliep <klaus.schl...@gmail.com> > Dear Jian-Feng, > > you can use the function plotBS. plotBS plots a tree and adds the > support values (in %). This function also silently returns this tree: > tree <- plotBS(fit$tree, bs) > # You can export than this tree using write.tree or write.nexus, e.g. > write.tree(tree) > > Regards, > Klaus > > > On 8/7/12, Mao Jianfeng <jianfeng....@gmail.com> wrote: > > Dear R-helpers and Klaus, > > > > I would like to know how to write out a tree file with bootstrap from > > phangorn package. That tree file could be in newick format or others. > > > > I am new for phylogenetic operation in R. Could you please give me any > > directions on that? Thanks in advance. > > > > Best wishes, > > Jian-Feng, > > > > ######## > > # as a example > > # I accomplished 1000 bootstrap simulation on a fit object (a maximum > > likelihood tree object) > > # how could I output a tree in newick format for tuning outside R? > > > > bs <- bootstrap.pml(fit, bs=1000, optNni=T, optInv=T, multicore=T) > > > -- Jian-Feng, Mao Post doc Dept. of Molecular Biology Max Planck Institute for Developmental Biology Spemannstrasse 37-39 72076 Tuebingen Germany Blog: http://maojf.blogspot.com/ [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
