[Biopython-dev] Calculating bootstrap values from a set of trees

[Cymon Cox]

Peter,

On 12 September 2011 16:18, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Sep 12, 2011 at 4:13 PM, Cymon Cox <cy at cymon.org> wrote:
> > Peter,
> >
> > I don't know of any stand alone software to automate the annotate of
> nodes
> > of a target tree with labels - I'm assuming you want to add labels (in
> this
> > case ML bootstrap support values) to a Newick tree description (eg an ML
> > optimal tree).
>
> Yes, or NJ bootstraps, or whatever.
>
> > Most wouldn't do this, but manually label the tree in a
> > graphics software when preparing the figure for publication.
>
> Huh. I guess it depends on the size of tree ;)
>


Well, yes. One of mine had >600 taxa - I didnt do it manually ;)



> > If you want support values for all nodes in your master/target tree, you
> > could loop over all the clades in your tree and use dendropy to help
> > calculate the bootstrap values for you bootstrap trees.
> >
> > Cheers, Cymon
>
> Thanks - looks like I'm not overlooking some really obvious tool
> to do this then.
>


Nothing obvious - but I have a vague recollection that Ive seen this as an
option in a tree graphics programme before - for the life of me I cant
remember which though! If I comes to me I'll let you know ;)

C.
-- 
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Cymon J. Cox