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 (http://rfam.xfam.org/).
To obtain Infernal releases, please visit eddylab.org/infernal.
to download and build the current source code release:
% wget http://eddylab.org/software/infernal/infernal.tar.gz % 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
you leave this optional
./configure argument off, the default prefix
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 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 v1.1.4, 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.