% tar zxf hmmer-3.1b2.tar.gz % cd hmmer-3.1b2 % ./configure % make % make check
The 'make check' is optional; it runs a test suite that checks for errors in the software.
All the binary tarballs include source code, plus a
directory containing precompiled binaries. Installing HMMER takes nothing other
than moving these binaries wherever you want them.
We believe HMMER compiles and runs on any POSIX-compliant system with an ANSI C99 compiler, including Mac OS/X, Linux, and any UNIX operating systems. For more installation and configuration options, see the Installation chapter of the User Guide (included in the package, and also linked in the documentation section on this site).
See the blog Cryptogenomicon for more information and discussion about HMMER3.
The theory behind profile HMMs: R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological sequence analysis: probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998.
Because we're an academic research group, HMMER comes with no promise of support. We are generally not able to respond individually to requests for help with the package, beyond the help already provided in HMMER's documentation. We do appreciate suggestions for better documentation, improvements, and bug reports.
Email email@example.com and please provide me with enough information that I can recreate the problem. Useful things to include are:
Without these pieces of information I have to make guesses and send mails back and forth with you to determine the cause of the issue, and then I get all frustrated and snippy with you because I'm usually pretty busy, and then you think I'm a jerk, and then I feel guilty and bad and have to go away and go running. Nobody wants all that drama.
Also, many questions are already covered in the HMMER documentation, so it may be worth browsing there first before sending an e-mail.