CARNA is a tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures.
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Dragos A. Sorescu, Mathias Moehl, Martin Mann, Rolf Backofen, and Sebastian Will
CARNA – alignment of RNA structure ensembles
Nucleic Acids Reseach, 40 no. W1 pp. W49-W53, 2012