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) > ______________________________________________ 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.
