| BlastHit | Blast-specific subclass of Bio::Search::Hit::GenericHit |
| Fasta | Hit object specific for Fasta-generated hits |
| GenericHit | A generic implementation of the Bio::Search::Hit::HitI interface |
| HMMERHit | A Hit module for HMMER hits |
| HitFactory | A factory to create Bio::Search::Hit::HitI objects |
| HitI | Interface for a hit in a similarity search result |
| HmmpfamHit | A parser and hit object for hmmpfam hits |
| PsiBlastHit | Bioperl BLAST Hit object |
| PullHitI | Bio::Search::Hit::HitI interface for pull parsers. |