| AlignIO | Handler for AlignIO Formats |
| AnalysisI | An interface to any (local or remote) analysis tool |
| AnalysisParserI | Generic analysis output parser interface |
| AnalysisResultI | Interface for analysis result objects |
| AnnotatableI | the base interface an annotatable object must implement |
| AnnotationCollectionI | Interface for annotation collections |
| AnnotationI | Annotation interface |
| Biblio | A Bibliographic Query Service module |
| ClusterI | Cluster Interface |
| ClusterIO | Handler for Cluster Formats |
| DBLinkContainerI | Abstract interface for any object wanting to use
database cross references |
| DasI | DAS-style access to a feature database |
| DescribableI | interface for objects with human readable names and descriptions |
| FeatureHolderI | the base interface an object with features must implement |
| Graphics | Generate GD images of Bio::Seq objects |
| IdCollectionI | interface for objects with multiple identifiers |
| IdentifiableI | interface for objects with identifiers |
| JobI | |
| LocatableSeq | A Sequence object with start/end points on it
that can be projected into a MSA or have coordinates relative to another seq. |
| LocationI | Abstract interface of a Location on a Sequence |
| MapIO | A Map Factory object |
| OntologyIO | Parser factory for Ontology formats |
| Perl | Functional access to BioPerl for people who don't know objects |
| PrimarySeq | Bioperl lightweight Sequence Object |
| PrimarySeqI | [Developers] - Interface definition for a Bio::PrimarySeq |
| Range | Pure perl RangeI implementation |
| RangeI | Range interface |
| SearchDist | A perl wrapper around Sean Eddy's histogram object |
| SearchIO | Driver for parsing Sequence Database Searches (Blast,FASTA,...) |
| Seq | Sequence object, with features |
| SeqAnalysisParserI | Sequence analysis output parser interface |
| SeqFeatureI | Abstract interface of a Sequence Feature |
| SeqI | [Developers] - Abstract Interface of Sequence (with features) |
| SeqIO | Handler for SeqIO Formats |
| SeqUtils | Additional methods for PrimarySeq objects |
| SimpleAlign | Multiple alignments held as a set of sequences |
| Species | Generic species object |
| Taxonomy | Conversion used bt the Taxonomy classes |
| TreeIO | Parser for Tree files |
| UpdateableSeqI | Descendant of Bio::SeqI that allows updates |