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.
Parent program: blast
BLAST is a software for comparing a query sequence with a library or database of sequences. BLAST identifies library hits that resemble the query above a certain threshold. Different types of BLASTs are designed according to the query and database types and search specificity (nucleotide blast implemented by blastn, megablast anddiscontiguousmegablast algorithms, protein blast by algorithms blastp, psi-blast, phi-blast, delta-blast, and three mixed types – blastx, tblastn, tblastx). Some specialized BLAST search types are also provided.