These programs use profile hidden Markov models (profile HMMs) to model the primary structure consensus of a family of protein or nucleic acid sequences.
All HMMER programs give a brief summary of their command-line syntax and options if invoked without any arguments. When invoked with the single argument, -h (i.e., help), a program will report more verbose command-line usage information, including rarely used, experimental, and expert options. -h will report version numbers which are useful if you need to report a bug or problem to me.
Each HMMER program has its own man page briefly summarizing command line usage. There is also a user's guide that came with the software distribution, which includes a tutorial introduction and more detailed descriptions of the programs.
See http://hmmer.wustl.edu/ for on-line documentation and the current HMMER release.
In general, no command line options should be needed by beginning users. The defaults are set up for optimum performance in most situations. Options that are single lowercase letters (e.g. -a ) are "common" options that are expected to be frequently used and will be important in many applications. Options that are single uppercase letters (e.g. -B ) are usually less common options, but also may be important in some applications. Options that are full words (e.g. -verbose ) are either rarely used, experimental, or expert options. Some experimental options are only there for my own ongoing experiments with HMMER, and may not be supported or documented adequately.
In general, HMMER attempts to read most common biological sequence file formats. It autodetects the format of the file. It also autodetects whether the sequences are protein or nucleic acid. Standard IUPAC degeneracy codes are allowed in addition to the usual 4-letter or 20-letter codes.
For ease of using large stable sequence and HMM databases, HMMER looks for sequence files and HMM files in the current working directory as well as in system directories specified by environment variables.