The current version of HMMER


The current version is HMMER 3.1b1 (27 May 2013).

Source: [FTP] [HTTP] 5.8 MB MD5: e81b689fe1dd7625cff84c08cbead1fc
with Linux/Intel ia32 binaries: [FTP] [HTTP] 18.1 MB MD5: 4a1cf63b124ec1bd4e2ef61adc9ed8d6
with Linux/Intel x86_64 binaries: [FTP] [HTTP] 20.2 MB MD5: efeac94139775d7810fb92a0a299980f
with MacOSX/Intel binaries: [FTP] [HTTP] 13.5 MB MD5: d0f27f050604307581efa5ab82c6654e

If you are looking for older versions of the software, try the archive link at the top of the page.


Release notes and User's Guide: [PDF, 116 pages].

Briefly, to compile from source:

   % tar zxf hmmer-3.1b1.tar.gz
   % cd hmmer-3.1b1
   % ./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).

Subversion Access

Our current development trunk is available via Subversion. To get an anonymous, read-only checkout:

svn checkout hmmer

We welcome code contributions. It's best to give us patches against the development trunk, rather than against the release code (but we'll look at whatever you give us). For developers who've been donating good patches to us for a while, we'll grant write access to the repository.

Windows/Cygwin binaries

These binaries are compiled to run in Cygwin (a Linux emulator that can be installed in Windows; In our hands, they run cleanly in a default Cygwin install.

If you are uncomfortable running HMMER3.1 within Cygwin, you may download older HMMER3.0 binaries (graciously produced and provided by Sergey Smirnov at the NCBI) that run in Windows without a Cygwin dependency.

hmmer-3.1b1-cygwin.tar.gz: [FTP] [HTTP] 15MB MD5: a2457588a7e33542698b190252202dd4

Further Reading


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.