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

Peter Cock p.j.a.cock at googlemail.com
Mon Sep 12 15:18:32 UTC 2011

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 ;)

> 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.


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