HMMER: biological sequence analysis using profile HMMs
Latest commit 5e98c5c Jun 13, 2018
Failed to load latest commit information.
autobuild Removes impl_dummy, the dummy (nonvectorized portable C) implementation. Jun 4, 2018
contrib BUGTRAX updated and put in reverse chronological order May 26, 2009
documentation Small update to userguide, thanking FSF for the GCC Compile Farm. Jun 12, 2018
libdivsufsort Fixes for issue #141 and #120: compile fails on i586, ppc64be Jun 9, 2018
profmark Fixes for issue #141 and #120: compile fails on i586, ppc64be Jun 9, 2018
release-notes update to 3.2.1 release notes. Jun 12, 2018
src Fixes some compiler warnings on ppc64be. Jun 13, 2018
test-speed Updates to URLs following web site cleanup. Jun 7, 2018
testsuite Improves flock()'ing in the test. Jun 13, 2018
tutorial Revisions to user guide in progress. May 26, 2018
.gitignore Updates, especially for recent Easel changes. Jun 5, 2017
INSTALL Updates versioning to 3.2.1, including user guide and its inclusions. Jun 11, 2018
LICENSE Updates version, date in INSTALL, LICENSE, May 30, 2018 Fixes for issue #141 and #120: compile fails on i586, ppc64be Jun 9, 2018 HMMER 3.2.1. Jun 13, 2018
config.guess Overhauls how 'make install' works. Apr 3, 2018
config.sub Overhauls how 'make install' works. Apr 3, 2018 Fixes iss #142, compilation fails ungracefully on ppc64le Jun 12, 2018
install-sh Incorporated Lindahl and IBM/Cheng changes, for Altivec Jan 26, 2005 Fixes the fix for issue #117; hmmsim segfault. Jun 2, 2018

HMMER - biological sequence analysis using profile HMMs

HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called "profile hidden Markov models" (profile HMMs). HMMER is used by many protein family domain databases and large-scale annotation pipelines, including Pfam and other members of the InterPro Consortium.

To obtain HMMER releases, please visit

To participate in HMMER development, visit us at github. HMMER development depends on the Easel library, also at github.

to download and build the current source code release:

   % wget
   % tar zxf hmmer.tar.gz
   % cd hmmer-3.2.1
   % ./configure --prefix /your/install/path
   % make
   % make check                 # optional: run automated tests
   % make install               # optional: install HMMER programs, man pages
   % (cd easel; make install)   # optional: install Easel tools

Executable programs will be installed in /your/install/path/bin. If you leave this optional ./configure argument off, the default prefix is /usr/local.

Files to read in the source directory:

  • INSTALL - brief installation instructions.
  • Userguide.pdf - the HMMER User's Guide.

To get started after installation, see the Tutorial section in the HMMER User's Guide (Userguide.pdf).

to clone a copy of HMMER3 source from github:

The tarball way, above, is a better way to install HMMER (it includes a precompiled Userguide.pdf, for example), but you can also clone our github repo. You need to clone both the HMMER and Easel repositories, as follows:

   % git clone
   % cd hmmer
   % git clone
   % autoconf

and to build:

   % ./configure
   % make

Our git workflow includes three main branches:

  • master is the stable branch for HMMER3 releases (including when H3 is released as a library inside Infernal)
  • develop is the HMMER3 development branch
  • h4-develop is the HMMER4 development branch.

To build the most recent official release, leave both HMMER and Easel on their default master branch. To contribute to HMMER3 development, you want to be on the develop branches.

to report a problem:

Visit our issues tracking page at github.