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 many members of the InterPro Consortium.
To obtain HMMER releases, visit hmmer.org.
To participate in HMMER development, visit us at github. HMMER development also depends on the lab's Easel library, at github.
% wget http://eddylab.org/software/hmmer/hmmer.tar.gz
% tar zxf hmmer.tar.gz
% cd hmmer-3.4
% ./configure --prefix /your/install/path # replace /your/install/path with what you want, obv
% 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:
To get started after installation, see the Tutorial section in the HMMER User's Guide (Userguide.pdf).
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 https://github.com/EddyRivasLab/hmmer
% cd hmmer
% git clone https://github.com/EddyRivasLab/easel
% autoconf
and to build:
% ./configure
% make
Our git workflow includes three main branches:
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.
Visit our issues tracking page at github.