HMMER User's Guide

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Command line options

If you forget the command-line syntax or available options of any of the programs, you can type the name of the program with no other arguments and get a short help message, including summaries of the common options.

Commonly used options are generally small letters, like -a. More infrequently used options are generally large letters, like -A. Expert or experimental options are generally in the GNU long form, like -null2.

If you call any program with an option -h, you get an augmented help message, including version info (the software version number is helpful if you report bugs or other problems to me) and a complete summary of all the available options, including rarely used and expert/experimental ones.