R help - Aug 2012 - 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-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)

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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)
>