Scoring schemes of different nucleotide versus nucleotide search algorithms from the NCBI blast pages.

Megablast is supposed to perform best in comparisons of closely related sequences with identities beyond 95%, whereas discontiguous megablast and the slower blastn algorithm should be better suited for cross-species comparisons. All blast types used a default expectancy threshold of 10.
1, settings of discontiguous megablast differed from previously reported settings [64].