formatdb is used to index protein or nucleotide databases so that they are formatted for searching using blastall.

formatdb 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.