[BioPython] parsing phylogenetic trees in Python

[Catherine Letondal]

Gregory Singer wrote:
> 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

Hi Greg,

Let me explain my question further: we are about to develop a module to follow
the biopython parsing framework (with consumers, etc...) as a student project.
(So, for now we do not intend to run phylogenetic analyses from alignments - to
answer Jan suggestion - and we are interested in a component approach). 

Gregory's package seems to be a good starting point for code to provide
standard operations on trees encoded in Python, but there is no parsing, I am right 
Gregory?


--
Catherine Letondal -- Pasteur Institute Computing Center