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 1.1.4 [9 Dec 2020].




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Infernal is open source software, freely distributed under the terms of a standard BSD (Berkeley Software Distribution) license..

Other useful Infernal resources:

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Internal benchmark:

Further reference:

Archived releases:

For reproducing published results, the following archived older versions may be of interest:

Release Date Download Notes
1.1.3 Nov 2019 [infernal-1.1.3.tar.gz] First version where cmscan and cmpress worked for non-calibrated models.
1.1.2 Jul 2016 [infernal-1.1.2.tar.gz] First version with cmscan capable of handling long sequences (e.g. chromosomes).
1.1.1 Jul 2014 [infernal-1.1.1.tar.gz] Version used for the Rfam 12.0 paper: (Nawrocki, 2015)
1.1 Oct 2013 [infernal-1.1.tar.gz] 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] 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] Version that reproduces the results in Eric Nawrocki's thesis, (Nawrocki, 2009)
1.0 Jan 2009 [infernal-1.0.tar.gz] Version described in the first "official" release paper, (Nawrocki et al., 2009)
0.81 May 2007 [infernal-0.81.tar.gz] First version with E-values and MPI parallelization.
0.72 Jan 2007 [infernal-0.72.tar.gz] Version used for the published version of the QDB algorithm paper (Nawrocki and Eddy, 2007)
0.71 Nov 2006 [infernal-0.71.tar.gz] Version used in the submitted version of the QDB algorithm manuscript (Nawrocki and Eddy, 2007)
0.7 Dec 2005 [infernal-0.7.tar.gz] Entropy weighting incorporated. This version was used by Paul Gardner and Eva Freyhult in their BRaliBaseIII benchmark.
0.6 Nov 2005 [infernal-0.6.tar.gz] Mixture Dirichlets incorporated, under pressure from Paul Gardner and Eva Freyhult's ongoing benchmarking work.
0.55 Apr 2003 [infernal-0.55.tar.gz] First version with documentation. Rfam 2.0 through Rfam 7.0 are based on 0.5x code (Griffiths-Jones et al, 2005)
0.4 Aug 2002 [infernal-0.4.tar.gz] cmalign first appears, and was used for final work on Rfam 1.0.
0.3 Jul 2002 [infernal-0.3.tar.gz] Version used for the first Rfam release (Griffiths-Jones et al, 2003)
0.1 Apr 2002 [infernal-0.1.tar.gz] Version used in the divide and conquer algorithm paper (Eddy, 2002)

Eddy/Rivas Laboratory
Last modified: Thu Dec 10 07:53:24 2020