[BioPython] parsing phylogenetic trees in Python

[Frank Kauff]

Hi all,

we are currently writing a Nexus parser, which also includes a tree
class. It's all still very alpha. So far, trees are represented as
nested lists (like the newick format itself), but also as a linked list
of nodes using a node class, where each node points to one parent
(=ancestor) and to multiple child nodes. This structure makes rerooting,
test for monophyly etc. fairly easy. 
If this would already be helpful, I'd be glad to send it to you (or
anybody who'd like to check it out). 

Frank


On Wed, 2004-02-25 at 02:41, Catherine Letondal wrote:
> Hi,
> 
> 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?
> 
> Thanks in advance,
-- 
Frank Kauff
Dept. of Biology
Duke University
Box 90338
Durham, NC 27708
USA

Phone 919-660-7382
Fax 919-660-7293