Structural RNA alignment by multi-objective optimization: RNA-Pareto
Please also see our corresponding publication:
Schnattinger T, Schöning U, Marchfelder A, Kestler HA. RNA-Pareto: Interactive Analysis of Pareto-optimal RNA Sequence-Structure Alignments. Bioinformatics 29(23): 3102-4, 2013. https://doi.org/10.1093/bioinformatics/btt536