[Biopython-dev] Rerooting a tree with Bio.Phylo

[Brad Chapman]

Eric, Peter and Cymon;

> I've got a real example of a simple tree manipulation that I would
> like to handle via your new module. I have a (small) unrooted tree from a
> gene family in Newick format, which by construction includes an
> out-group (the same gene but from a more distant organism). I would like to
> reroot the tree so that this out-group is at the basal level.

Really enjoying the discussion on this. It's a bit outside my area
of expertise but I stumbled across DendroPy this weekend:

http://packages.python.org/DendroPy/index.html

which has a reroot_at function that might be worth looking into:

http://github.com/jeetsukumaran/DendroPy/blob/master/dendropy/dataobject/tree.py

Hope this helps,
Brad