Chapter 13. NCBI-BLAST Reference

This chapter describes the parameters and options for the NCBI suite of BLAST programs. The NCBI distribution includes the blastall program, plus several ancillary programs that are either necessary for blastall (e.g., formatdb) or provide other BLAST-like searches that aren't included within blastall (e.g., blastpgp and blastclust). This reference also describes the various command-line parameters for the most important executables.