Current user guide & release notes

Briefly, to compile from source:

  % 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 binaries/ 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).

Further Reading


See the blog Cryptogenomicon for more information and discussion about HMMER3.

  • Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 7:e1002195 (2011)
  • Eddy SR. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput. Biol. 4:e1000069 (2008)
  • Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 23:205-11 (2009).
  • Other publications about HMMER

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.

Reporting bugs

Email and please provide me with enough information that I can recreate the problem. Useful things to include are:

  • Input data (or examples, a small test case sufficient to recreate the problem).
  • Information about the operating system you are using (e.g. cat /proc/cpuinfo or uname -a
  • Which version of HMMER you're using, and whether you compiled from source or used a binary distro.

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.