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Infernal - inference of RNA secondary structure alignments

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 (

To obtain Infernal releases, please visit

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.

to download and build the current source code release:

   % wget
   % tar zxf infernal.tar.gz
   % cd infernal-1.1.4
   % ./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).

to clone a copy of Infernal source from github:

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
   % cd infernal
   % git clone
   % git clone
   % 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 v1.1.4, you'll want to checkout the corresponding tags from the HMMER and Easel branches.

   % cd infernal
   % cd hmmer
   % git checkout infernal-1.1.4
   % cd easel
   % git checkout infernal-1.1.4

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.

to report a problem:

Visit our issues tracking page at github.