makemat is a primary profile preprocessor. It converts a collection of binary profiles, created by the -C option of psi-blast, into portable ASCII form. See also copymat

makemat 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.