| AlignSlice | An AlignSlice can be used to map genes and features from one species onto another one |
| AlignedMember | DESCRIPTION of Object |
| Attribute | |
| BaseRelation | |
| ConservationScore | Stores conservation scores |
| ConstrainedElement | constrained element data produced by Gerp |
| DnaFrag | Defines the DNA sequences used in the database. |
| DnaFragRegion | dnafrag region on one species |
| Domain | |
| Family | |
| GenomeDB | DESCRIPTION of Object |
| GenomicAlign | Defines one of the sequences involved in a genomic alignment |
| GenomicAlignBlock | Alignment of two or more pieces of genomic DNA |
| GenomicAlignGroup | Defines groups of genomic aligned sequences |
| GenomicAlignTree | DESCRIPTION of Object |
| Homology | Homology between two proteins |
| Member | |
| MethodLinkSpeciesSet | Relates every method_link with the species_set for which it has been used |
| NCBITaxon | DESCRIPTION of Object |
| NestedSet | DESCRIPTION of Object |
| PeptideAlignFeature | |
| ProteinTree | DESCRIPTION of Object |
| SitewiseOmega | DESCRIPTION of Object |
| Subset | DESCRIPTION of Object |
| SyntenyRegion | Synteny region |
| Taxon | DESCRIPTION of Object |