The current version of HMMER


The current version is HMMER 3.1b2 (05 March 2015).

Source: [FTP] [HTTP] 5.8 MB MD5: c8c141018bc0ccd7fc37b33f2b945d5f
with Linux/Intel ia32 binaries: [FTP] [HTTP] 18.1 MB MD5: ce11c2762f35fb9be8614dd4848b2ac1
with Linux/Intel x86_64 binaries: [FTP] [HTTP] 20.2 MB MD5: 44ea3dc8b50657101ab9ba1807ccfcd3
with MacOSX/Intel binaries: [FTP] [HTTP] 13.5 MB MD5: 1251d66d29166032524e515efa331836

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-3.1b2.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).

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-3.1b2-cygwin32.tar.gz: 32-bit [FTP] [HTTP] 15MB MD5: 6fe4c2c4eeaebdad9024390195f50059
hmmer-3.1b2-cygwin64.tar.gz: 64-bit [FTP] [HTTP] 16MB MD5: b5e265550be62a395dc475aee158a3f4

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.