Like other programs in the blast package, blastall is a command line program with no graphic user interface (GUI). We control the program through command line option switches issued in a terminal window. These options instruct blastall what program function, query, and database to use. They also control the search sensitivity, the result format, and the name of the output file, etc. Typing "blastall -" followed by a return key stroke will display the blastall parameters along with short descriptions on each option. In this section, we will provide a much more detailed explanation for these parameters.