Search for matches to a covariance model in RNA sequences, or align RNA sequences to a covariance model. Covariance models use a combination of primary structure (nucleotide sequence) and secondary structure (base pairing) to model non-protein-coding RNA families. This package is a thin wrapper around the Infernal package, which is not included and needs to be installed independently. Functions to read, write, and manipulate multiple sequence alignments in Stockholm format are also included.
