Package edu.rit.compbio.seq contains parallel programs for biological sequence alignment.

The following programs search a protein sequence database to find matches for a query protein sequence:

- Class FindProteinSeq
- Class FindProteinHyb
- Class FindProteinHyb2

The following class encapsulates a protein sequence database; it includes a main program that prepares a database index file used by the above protein sequence database search programs:

- Class ProteinDatabase

The other classes are used by the above programs.