Re: [R] 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,

Re: [R] how to write out a tree file with bootstrap from phangorn package

Dear Klaus, Thanks a lot for your kind reply. That is really valuable for me. Best wishes, Jian-Feng, 2012/8/7 Klaus Schliep > 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 <

[R] how to write out a tree file with bootstrap from phangorn package

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-Fe