Pros and Cons of a large single distribution
This is a large monolithic set of modules that seems overwhelming to many people. Some folks have advocating splitting things up into different pieces, but most of the developers find this a difficult thing to do because we are intentionally re-using things. ... Plus the nightmare of doing a release - when it depends on an up-to-date version of modules from three sub-packages. We have a hard enough time releasing bioperl-run and bioperl-db at the same time as a new bioperl-core.
Google_Summer_of_Code#Major_BioPerl_reorganization intends to break up the monolith.
The latest code
The latest, and not completely tested, code can be viewed here:
You can download it by following the instructions on the Using Git page. The repository name is bioperl-live.