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CentroidFold based on a generalized centroid estimator is one of the most accurate tools for predicting RNA secondary structures. See the original paper for the details of the algorithm.

CentroidFold Web Server
Link to the original paper
README for the software
CentroidFold package contains three software: CentroidFold (RNA secondary structure prediction), CentroidAlifold (Common secondary structure prediction of RNAs) and CentroidHomfold (RNA secondary structure prediction with homologous sequences)
Each directory contains figures (PDF format) in the paper as follows: single: secondary structure predictions from an RNA sequence aln : common secondary structure predictions aln-n : common secondary structure predictions of 2,4,6,8,10 sequences
Help for Web Application
CentroidFold lets you get a predicted secondary structure for a given RNA sequence and a predicted common secondary structure for a given multiple-alignment.
Help Figures

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