megablast implements a greedy algorithm for the DNA sequence gapped alignment search. Megalast can only work with DNA sequences, thus you can only use megablast to search a nucleotide database with nucleotide sequences.

megablast 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.