Infernal: inference of RNA alignments


Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

The latest release of Infernal is 1.1.1 [23 July 2014].




Contact us:

Rfam CMs:

Internal benchmark:

Further reference:

Archived releases:

For reproducing published results, the following archived older versions may be of interest. Other releases are also archived on our FTP site, but these are the main mileposts:

Release Date Download Notes
1.1 Oct 2013 [infernal-1.1.tar.gz, 18.3 MB] First stable 1.1 release; the version described in the 2013 Bioinformatics application note: (Nawrocki and Eddy, 2013)
1.0.2 Oct 2009 [infernal-1.0.2.tar.gz, 15.2 MB] Last release before the major 1.1 update. This was the "current" version for nearly three years.
1.0.1 Oct 2009 [infernal-1.0.1.tar.gz, 15.2 MB] Version that reproduces the results in Eric Nawrocki's thesis, (Nawrocki, 2009)
1.0 Jan 2009 [infernal-1.0.tar.gz, 15.0 MB] Version described in the first "official" release paper, (Nawrocki et al., 2009)
0.81 May 2007 [infernal-0.81.tar.gz, 6.5 MB] First version with E-values and MPI parallelization.
0.72 January 2007 [infernal-0.72.tar.gz, 6.0 MB] Version used for the published version of the QDB algorithm paper (Nawrocki and Eddy, 2007)
0.71 November 2006 [infernal-0.71.tar.gz, 6.0 MB] Version used in the submitted version of the QDB algorithm manuscript (Nawrocki and Eddy, 2007)
0.7 December 2005 [infernal-0.7.tar.gz, 4.3 MB] Entropy weighting incorporated. This version was used by Paul Gardner and Eva Freyhult in their BRaliBaseIII benchmark.
0.6 November 2005 [infernal-0.6.tar.gz, 4.3 MB] Mixture Dirichlets incorporated, under pressure from Paul Gardner and Eva Freyhult's ongoing benchmarking work.
0.55 April 2003 [infernal-0.55.tar.gz, 763 KB] First version with documentation. Rfam 2.0 through Rfam 7.0 are based on 0.5x code (Griffiths-Jones et al, 2005)
0.4 August 2002 [infernal-0.4.tar.gz, 443 KB] cmalign first appears, and was used for final work on Rfam 1.0.
0.3 July 2002 [infernal-0.3.tar.gz, 431 KB] Version used for the first Rfam release (Griffiths-Jones et al, 2003)
0.1 April 2002 [infernal-0.1.tar.gz, 402 KB] Version used in the divide and conquer algorithm paper (Eddy, 2002)

Sean Eddy
EPN, Thu Apr 16 15:17:49 2015