[BioPython] parsing phylogenetic trees in Python

[Jason Stajich]

I've also written bits and pieces of tree stuff in Bioperl as well - you are
more than welcome to steal from the perl modules if you like.

It is all still improving and being developers so live CVS code is better
than the most recent release I expect.

Tree Parsers-
  Bio::TreeIO (nexus, newick, nhx)
MSA parsers
  Bio::AlignIO (nexus,phylip formats)

Tree code
  Bio::Tree::
   - building random trees (part of which is used for the coalescent sims)
   - some simple tests and statistics like most recent common ancestor,
     tests of monophyly, etc.

On Wed, 25 Feb 2004, Gregory Singer wrote:

> Quoting Catherine Letondal <letondal at pasteur.fr>:
>
> > 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?
>
> Ack! Please call me Greg. Only my mother calls me Gregory. Anyway, you're right
> about the lack of BioPython-style parsing, which would be a nice addition (and
> probably not that difficult?)
>
>  - Greg
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu