blastn is part of the new blast+ package from the NCBI.

blastn searches a nucleotide database using a nucleotide query.

Help on the options available can be found by typing blastn -help

blastn understands the concept of tasks. The following tasks can be requested using the -task option and giving one of the following as the argument:

• blastn: Traditional BLASTN requiring an exact match of 11
• blastn-short: BLASTN program optimized for sequences shorter than 50 bases
• megablast: Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequencesdc-megablast
• Discontiguous megablast used to find more distant (e.g., interspecies) sequences

Indexed searches for megablast are available and are faster than regular megablast. The application to generate the database indices is called makembindex.