| Allele | A single allele of a nucleotide variation. |
| AlleleFeature | A genomic position for an allele in a sample. |
| AlleleGroup | Ensembl representation of a grouping of alleles (aka haplotype). |
| ConsequenceType | Bio::EnsEMBL::Variation::ConsequenceType |
| Genotype | Abstract base class representing a genotype |
| Individual | A single member of a population. |
| IndividualGenotype | Module representing the genotype of a single individual at a single position |
| IndividualGenotypeFeature | Module representing the genotype of a single individual at a single position |
| LDFeatureContainer | A container with all the ld values for quick access |
| Population | A population represents a phenotypic group, ethnic group, set of individuals used in an assay, etc. |
| PopulationGenotype | Module for a genotype represented in a population. |
| ReadCoverage | A coverage reagion for a read. |
| ReadCoverageCollection | A collection of coverage reagion for a read. |
| Sample | An abstract base class to represent Population, Individual or Strain |
| TranscriptVariation | Bio::EnsEMBL::Variation::TranscriptVariation |
| Variation | Ensembl representation of a nucleotide variation. |
| VariationAnnotation | A genotype phenotype annotation for a nucleotide variation. |
| VariationFeature | A genomic position for a nucleotide variation. |
| VariationGroup | Ensembl representation of a grouping of variations (aka haplotype set). |
| VariationGroupFeature | A genomic position for a variation group (aka haplotype block). |