HMMER biosequence analysis using profile hidden Markov models

Download

The current version is HMMER 3.0 (28 March 2010).

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

Documentation

Briefly, to compile from source:

   % tar zxf hmmer-3.0.tar.gz
   % cd hmmer-3.0
   % ./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 https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk 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 binaries

These binaries have been graciously produced and provided by Sergey Smirnov at the NCBI. Please see the readme.txt included within the zip file for installation hints and contact details.

Further Reading