SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework (original) (raw)
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).