Evo Fold
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Evofold: http://www.cbse.ucsc.edu/~jsp/EvoFold/
Evo Fold is a comparative method for identifying functional RNA structures in multiple-sequence alignments. It is based on a probabilistic model-construction called a phylo-SCFG and exploits the characteristic differences of the substitution process in stem-pairing and unpaired regions to make its predictions. Each prediction consists of a specific secondary structure and a folding potential score.
