[BioPython] parsing phylogenetic trees in Python
fkauff at duke.edu
Thu Feb 26 14:37:18 EST 2004
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).
On Wed, 2004-02-25 at 02:41, 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?
> Thanks in advance,
Dept. of Biology
Durham, NC 27708
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