[BioPython] parsing phylogenetic trees in Python

[Jan T. Kim]

On Wed, Feb 25, 2004 at 08:41:09AM +0100, Catherine Letondal wrote:

> I'm aware of several tools and packages dealing with phylogenetics and
> Phylip-Nexus files such as:
> 
> p4 http://www.nhm.ac.uk/zoology/external/p4.htm
> 
> Mavric http://www.bioinformatics.org/mavric/
> 
> PyPhy http://www.cbs.dtu.dk/staff/thomas/pyphy/
> 
> However, I haven't found any official Python
> or biopython module for a parser like the ones available
> in the biopython parsing framework.
> 
> 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?

Perhaps, we should discuss what this parser should achieve. Writing a
parser for "New Hampshire" (aka PHYLIP) tree files is reasonably easy
and doesn't require BioPython by itself. It would, however, be interesting
to use BioPython as a framework which would also support integration
with other data. For example, it would be nice to be able to read a
set of sequences (e.g. from a GenBank file), to compute a tree using
PHYLIP, and to determine in that tree what the last common ancestor of
two sequences of special interest is, and what other sequences belong
to the group (subfamily) of descendants of that last common ancestor.

I have once started to write some stuff for such purposes, and I'd be
interested in having, and -- time permitting -- programming something
like this in BioPython.

Greetings,
Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
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