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 hmmer.org.

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

Don't use github as a source of "official" HMMER release code. Our release tarballs bundle up some convenient stuff that you have to be able to create for yourself if you're trying to do it from our github repository.

to download and build the current source code release:

Various tarballs of pre-compiled executables and source code for a variety of systems are available at hmmer.org, but it is also straightforward to download and build from source on most systems:

   % wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz
   % tar zxf hmmer-3.1b2.tar.gz
   % cd hmmer-3.1b2
   % ./configure --prefix /your/install/path
   % make
   % make check
   % make install

Executable programs will be installed in /your/install/path/bin.

Files to read in the top-level 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:

You need to clone both the HMMER and Easel repositories, as follows:

   % git clone https://github.com/EddyRivasLab/hmmer
   % cd hmmer
   % git clone https://github.com/EddyRivasLab/easel
   % git checkout develop
   % (cd easel; git checkout develop)
   % 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 contribute to HMMER3 development, you want to be on the develop branch.

to report a problem:

Visit our issues tracking page at github.