how to write out a tree file with bootstrap from phangorn package
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.mao at 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)