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megablast

task:  megablast versus blastn

Task types define optimal settings (word-size, gap values) for comparing inner- or inter-species sequences.

-task megablast (default): for comparison within the same species (fast)
blastn  -query gene.ffn      -subject genome.fna    -task megablast

-task blastn: for comparison of sequences from different species (slow, but finds more hits)
blastn  -query speciesA.fna  -subject speciesB.fna  -task blastn

"The “megablast” task is optimized for intraspecies comparison as it uses a large word-size of 28bp, whereas “blastn” is better suited for interspecies comparisons with a shorter word-size of 11bp." [ncbi]

Alternatively, word-size and gap values can be adapted manually using the → command options.