Infernal is an implementation of covariance models (CMs), which are statistical models of RNA secondary structure and sequence consensus. You give Infernal a multiple sequence alignment of a conserved structural RNA family, annotated with the consensus secondary structure. The "cmbuild" program builds a statistical profile of your alignment. That CM can be used as a query in a database search to find more homologs of your RNAs (the "cmsearch" program). You can also use a CM of a representative alignment of your sequence family to create a larger consensus alignment of any number of RNAs (the "cmalign" program). Infernal is the software engine underlying the Rfam RNA database (http://rfam.xfam.org/).

To obtain Infernal releases, please visit eddylab.org/infernal.

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

   % wget http://eddylab.org/software/infernal/infernal.tar.gz
   % tar zxf infernal.tar.gz
   % cd infernal-1.1.5
   % ./configure --prefix /your/install/path
   % make
   % make check                 # optional: run automated tests
   % make install               # optional: install Infernal programs, man pages
   % (cd hmmer; make install)   # optional: install HMMER programs
   % (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 Infernal User's Guide.

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

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

   % git clone https://github.com/EddyRivasLab/infernal
   % cd infernal
   % git clone https://github.com/EddyRivasLab/hmmer
   % git clone https://github.com/EddyRivasLab/easel
   % autoconf

and to build:

   % ./configure
   % make

Our git workflow includes two main branches:

• master is the stable branch for Infernal releases
• develop is the Infernal development branch

To build the most recent official release, currently v1.1.5, you'll want to checkout the corresponding tags from the HMMER and Easel branches.

   % cd infernal
   % cd hmmer
   % git checkout infernal-1.1.5
   % cd easel
   % git checkout infernal-1.1.5

To contribute to Infernal 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.