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.

Other files to read in the top-level source directory:

• INSTALL - brief installation instructions.
• Userguide.pdf - the HMMER User's Guide.
• LICENSE - copyright and license information

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

To obtain HMMER releases, please visit: http://hmmer.org

To participate in HMMER development, visit us at github: https://github.com/EddyRivasLab/hmmer

HMMER depends on the Easel library, also hosted at github: https://github.com/EddyRivasLab/easel

To clone your own copy of HMMER3 source code repository for the first time:

   $ git clone https://github.com/EddyRivasLab/hmmer
   $ cd hmmer
   $ git clone https://github.com/EddyRivasLab/easel
   $ git checkout h3-develop
   $ (cd easel; git checkout develop)
   $ ln -s easel/aclocal.m4 aclocal.m4
   $ autoconf

and to build:

   $ ./configure
   $ make

We have just switched to a "git flow" workflow. We have three active branches:

• h3-master is to become the stable HMMER3 release branch.
• h3-develop is the HMMER3 development branch
• master, for historical reasons, is the HMMER4 development branch.

To contribute to HMMER3 development, you want to be on the h3-develop branch, which is where we are currently integrating feature branches. We don't currently recommend that you use the master branch where H4 is getting assembled. For more information, see the HMMER wiki.