Major Bioperl Module Groups
| Modules | Description |
| Bio∷Seq | Sequences and their properties |
| Bio∷SeqIO | Sequence data input/output |
| Bio∷Index | Flat-file sequence database indexing and retrieval |
| Bio∷DB | Remote database access for sequences and references via HTTP |
| Bio∷DB∷GFF | SQL GFF database for DAS and GBrowse backends |
| Bio∷SeqFeature | Annotations or features that have a sequence location |
| Bio∷Annotation | Generic annotations such as Comments and References |
| Bio∷AlignIO, Bio∷SimpleAlign | Multiple sequence alignments and their Input/Output |
| Bio∷LiveSeq, Bio∷Variation | Sequence variations and mutations |
| Bio∷Search, Bio∷SearchIO | Sequence database searches and their Input/Output |
| Bio∷Tools | Miscellaneous analysis tools |
| Bio∷Tools∷Run | Wrapper for executing local and remote analyses |
| Bio∷Tree, Bio∷TreeIO | Phylogenetic trees and their Input/Output |
| Bio∷Structure | Protein structure data |
| Bio∷Map, Bio∷MapIO | Biological maps and their Input/Output |
| Bio∷Biblio, Bio∷DB∷Biblio | Bibliographic References and Database retrieval |
| Bio∷Graphics | Graphical displays of sequences |