| Chain | Mapping locations through a chain of coordinate mappers |
| Collection | Noncontinuous match between two coordinate sets |
| ExtrapolatingPair | Continuous match between two coordinate sets |
| GeneMapper | transformations between gene related coordinate systems |
| Graph | Finds shortest path between nodes in a graph |
| MapperI | Interface describing coordinate mappers |
| Pair | Continuous match between two coordinate sets |
| Result | Results from coordinate transformation |
| ResultI | Interface to identify coordinate mapper results |
| Utils | Additional methods to create Bio::Coordinate objects |