| BlastHSP | Bioperl BLAST High-Scoring Pair object |
| FastaHSP | HSP object for FASTA specific data |
| GenericHSP | A "Generic" implementation of a High Scoring Pair |
| HMMERHSP | A HSP object for HMMER results |
| HSPFactory | A factory to create Bio::Search::HSP::HSPI objects |
| HSPI | Interface for a High Scoring Pair in a similarity search result |
| WABAHSP | HSP object suitable for describing WABA alignments |