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November 26, 2020 16:16
September 14, 2020 13:49
November 26, 2020 16:16

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-3.3.2
   % ./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. If you want to send us a pull request on GitHub, please base your changes on our develop branches.

to report a problem:

Visit our issues tracking page at github.