[Biopython-dev] GSoC code+documentation review: PhyloXML for Biopython

Peter biopython at maubp.freeserve.co.uk
Sun Jul 5 08:52:38 UTC 2009

On Sat, Jul 4, 2009 at 8:38 PM, Brad Chapman<chapmanb at 50mail.com> wrote:
> I really like the idea of exploring interoperability with other
> Biopython tree representations and generalizing there. In addition to
> the Tree class in Bio.Nexus, the PyCogent tree representation looks
> generalized:
> http://pycogent.svn.sourceforge.net/viewvc/pycogent/trunk/cogent/core/tree.py?view=markup

There is also Thomas Mailund's Newick Tree module, which provides
yet another perspective on trees, and various things you can do with
them (his visitor stuff is cool once you figure it out). If you haven't
looked it this, it might be worth a play as well for ideas. I've actually
used this more than Bio.Nexus as it predates it ;)


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