| Archiver | create gene_archive and peptide_archive |
| BaseObject | base object for IdMapping objects |
| Cache | a cache to hold data objects used by the IdMapping application |
| Entry | object representing a ScoredMappingMatrix entry |
| ExonScoreBuilder | |
| GeneScoreBuilder | |
| InternalIdMapper | |
| MappingList | object holding a list of Entries |
| ResultAnalyser | analyse stable Id mapping results |
| ScoreBuilder | score builder base class |
| ScoredMappingMatrix | object holding a list of scored Entries |
| Serialisable | base class for serialisable objects |
| StableIdMapper | |
| SyntenyFramework | framework representing syntenic regions across the genome |
| SyntenyRegion | object representing syntenic regions |
| TinyExon | lightweight exon object |
| TinyFeature | lightweight feature object |
| TinyGene | lightweight gene object |
| TinyTranscript | lightweight transcript object |
| TinyTranslation | lightweight translation object |
| TranscriptScoreBuilder |