| 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 |
| FeatureIO | Handler for FeatureIO |
| HandlerBaseI | Interface class for handler methods which interact with any
event-driven parsers (drivers). |
| IdCollectionI | interface for objects with multiple identifiers |
| IdentifiableI | interface for objects with identifiers |
| JobI | |
| LocatableSeq | A Bio::PrimarySeq 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 |
| NexmlIO | stream handler for NeXML documents |
| OntologyIO | Parser factory for Ontology formats |
| ParameterBaseI | Simple interface class for any parameter-related data such
as IDs, database name, program arguments, and other odds and ends. |
| Perl | Functional access to BioPerl for people who don't know objects |
| PhyloNetwork | Module to compute with Phylogenetic Networks |
| PrimarySeq | Bioperl lightweight Sequence Object |
| PrimarySeqI | Interface definition for a Bio::PrimarySeq |
| PullParserI | A base module for fast 'pull' parsing |
| 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 |
| SimpleAnalysisI | A simple interface to any (local or remote) analysis tool |
| Species | Generic species object. |
| Taxon | A node in a represented taxonomy |
| Taxonomy | representing Taxonomy. |
| TreeIO | Parser for Tree files |
| UpdateableSeqI | Descendant of Bio::SeqI that allows updates |
| WebAgent | A base class for Web (any protocol) access |