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.schliep@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.mao@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/

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