| Program name | Description | 
|---|
| profit | Scan one or more sequences with a simple frequency matrix | 
| prophecy | Create frequency matrix or profile from a multiple alignment | 
| prophet | Scan one or more sequences with a Gribskov or Henikoff profile | 
| seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file | 
| siggen | Generate a sparse protein signature from an alignment | 
| siggenlig | Generate ligand-binding signatures from a CON file | 
| sigscan | Generate hits (DHF file) from a signature search | 
| sigscanlig | Search ligand-signature library and writes hits (LHF file) |