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FOLDALIGN

http://foldalign.kvl.dk/

Description :
FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences.

NDB Tools

http://ndbserver.rutgers.edu/services/

Description :
The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.

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