[BioPython] parsing phylogenetic trees in Python

[Gregory Singer]

Quoting Catherine Letondal <letondal at pasteur.fr>:
> Does someone in this mailing-list know about a project for
> writing a parser (as a module) or is it so easy to do that
> nobody needs any?

I replied to Catherine personally about this, but I thought other members of the
list might also be interested. About four years ago I contributed a module to
BioPython called "TreeManip" that could do some basic Newick tree manipulations,
like re-rooting the tree, deleting clades, ladderizing, etc. Some time between
then and now it seems to have been dropped from BioPython, but I still use it in
my own research and although the code is rough and antiquated, it does seem to
work quite well.

The module is a little large to mail out to the whole list, but e-mail me if
you'd like a copy of it.

 - Greg