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SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

Figure 3

Sampling Alignment and Structure

We sample a new alignment by choosing a random window of the alignment that is devoid of base-pairs and by realigning it (step 1). We then sample a new RNA structure by removing a random set of helices from the given structure (step 2) and by adding a set of new helices (step 3).

Figure 3