[BioPython] Molecular phylogeny

[Jan T. Kim]

On Tue, Apr 17, 2001 at 06:47:59PM +0200, Andersson, Claes wrote:

> However, now I would like to get my hands dirty as well and since one my main 
> bioinformatics interests are molecular phylogeny I'm wondering if there are any 
> phylogeny tools out there for python (Mavric excluded)?
> 
> If not, I'd like to write some code for UPGMA, neighbours relation etc which 
> would fit seamlessly with the biopython suite (are wrappers preferred?). Does 
> this sound like a good idea to anybody?

Definitely. At least, I'd like to have such stuff, too.

I'm not sure what you mean by "wrappers", but I think this would fit
into the general BioPython concept (as far as I understand it, anyway)
of delegating the actual computation to external programs such as
BLAST, clustal etc.

It would be an obvious choice to write wrappers for the PHYLIP programs.

> Or has it already been done?

Actually, a diploma student I advised and I once wrote some wrappers
for the PHYLIP programs "neighbor" and "protpars", but that was before
I knew about BioPython.

> If so, 
> where can I find it?

Unfortunately, the stuff we hacked up back then got rather tightly
interwoven into the code developed during that thesis. I could
probably find this stuff somewhere, but I doubt that it's worth the
trouble, as the parser parts are probably difficult to modularize
out of the bulk... it's probably a cleaner start to implement parsers
following the BioPython concepts and then to build new wrappers on
top of these.

Greetinx, Jan
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