[Biopython-dev] Nexus parser and Newick tree format

[Peter]

Iddo Friedberg wrote:
> Hi all,
> 
> Good News: Frank Kauff & Cymon Cox has contributed a Nexus parser to 
> Biopython, for our next release. It's a mighty useful and nifty package 
> if you are into trees (the phylogenetic ones, not the ones in the 
> forest). He put a lot of effort into this to get this ready for 
> Biopython 1.40

This sounds really good.

I have been dealing with Newick trees (e.g. the .dnd files produced by 
Clustal) using the Python Newick module by Thomas Mailund 
(Bioinformatics Research Center, University of Aarhus):

http://www.daimi.au.dk/~mailund/newick.html

A bit of googling tells me that the NEXUS format incorporates the Newick 
treefile data plus additional text.

http://workshop.molecularevolution.org/resources/fileformats/tree_formats.php

Can/will the new Bio.Nexus module cope with "plain" Newick files as well 
as the more complicated Nexus format?

Peter

P.S. A trivial "bug", you have used "hsitorical" in class Tree, file 
Trees.py

-- 
PhD Student
MOAC Doctoral Training Centre
University of Warwick, UK