SimulFold 1.0 is a computer program for co-estimating an RNA structure including pseudo-knots, a multiple-sequence alignment and an evolutionary tree, given a set of evolutionarily related RNA sequences as input. In other words, you give SimulFold an initial alignment of RNA sequences as input and it will predict a consensus RNA structure which may include pseudo-knots while simultaneously estimating the sequence alignment and the evolutionary tree relating the RNA sequences. This means, in particular, that the input alignment need not be a manually curated alignment of high quality. SimulFold employs a Markov Chain Monte Carlo in order to sample from the joint posterior distribution of RNA structures, alignments and trees. A post-processing step is then used to cluster the sampled RNA structures into one RNA structure.
SimulFold paper and software: