CentroidAlifold: Accurate (common) secondary structure prediction for aligned RNA sequences. CentroidFold is one of the most accurate tools for predicting RNA secondary structures. It is based on the gamma-centroid estimator (Hamada et.al., 2009) for high-dimensional discrete spaces. Generally, a gamma-centroid estimator is slightly more accurate than an MEA estimator (Do et.al., 2005) under the same probability distribution. CentroidAlifold can predict common secondary structures for multiple alignments of RNA sequences by using an averaged gamma-centroid estimator (Hamada et al., 2010).

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  1. Fu, Haoyue; Yang, Lianping; Zhang, Xiangde: An RNA secondary structure prediction method based on minimum and suboptimal free energy structures (2015)