| Exception | Generic exception objects for Bioperl |
| HTTPget | module for fallback HTTP get operations when LWP:: is unavailable |
| IO | module providing several methods often needed when dealing with file IO |
| Root | Hash-based implementation of Bio::Root::RootI |
| RootI | Abstract interface to root object code |
| Storable | object serialisation methods |
| Version | provide global, distribution-level versioning |