[Biopython] Cogent package

[Brad Chapman]

Jeff;

> I have been working with with the biopython package for about the
> past year (formerly worked with perl and dabbled in bioperl a bit)
> and somehow the pycogent package didn’t even cross my radar. I just
> discovered it by accident in a code search on the web. So how does
> pycogent relate to and compare with biopython? It seems that the most
> recent release of cogent (1.4.1) is fairly mature and contains a large
> amount and diversity of code. 

PyCogent is definitely a useful library to have in your toolbelt.
It focuses a bit more on evolutionary and phylogenetic work, so will
give you extra functionality if you're working in those areas.
We'd hoped to develop formal interoperability with PyCogent,
and proposed a summer of code project along those lines:

http://biopython.org/wiki/Google_Summer_of_Code#Biopython_and_PyCogent_interoperability

but unfortunately didn't get funded this year. A few other useful
Python biology projects are:

bx-python: http://bitbucket.org/james_taylor/bx-python/wiki/Home
DendroPy: http://packages.python.org/DendroPy/
Pygr: http://code.google.com/p/pygr/

It would be cool to see the Python bioinformatics community develop
documentation and examples of using multiple toolkits together.

Brad