RNAG predicts consensus secondary structures for unaligned sequences. It uses a blocked Gibbs sampling algorithm, which has a theoretical advantage in convergence time. This algorithm iteratively samples from the conditional probability distributions P(Structure | Alignment) and P(Alignment | Structure).
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Donglai Wei, Lauren V. Alpert and Charles E. Lawrence
RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences
ioinformatics (2011) 27 (18): 2486-2493.