blastpgp performs gapped blastp searches, and can also be used to perform iterative searches in psi-blast and phi-blast mode.

blastpgp is one of the programs distributed along with the old blastall program by the NCBI. The NCBI recommends that people start using the programs of the blast+ package instead. Having said that, most documentation currently available still refers to blastall and the programs distributed with it.

The programs distributed with blastall include:

• bl2seq
• blast2
• blastall
• blastcl3
• blastclust
• blastpgp
• copymat
• fastacmd
• formatdb
• formatrpsdb
• impala
• makemat
• megablast
• rpsblast
• seedtop
• taxblast

The man pages for these provide further details.