Infernal, standing for "INFERence of RNA ALignment", is a tool for searching
DNA sequence database for RNA structure and sequence similarities.

It is based on Covariance Model (CM), which scores a combination of sequence
consensus and RNA secondary structure consensus, and thus is more capable of
identifying RNA homologs than using primary sequence profile.

The Rfam database of RNA families is based on Infernal. 

Citation:
Nawrocki & Eddy (2013) Infernal 1.1: 100-fold faster RNA homology searches,
Bioinformatics 29: 2933-2935.

WWW: http://eddylab.org/infernal/