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

Figure 5

Loglikelihood as a Function of the Steps in the MCMC Chain for the HDV set with and without Parallel Tempering

With parallel tempering (grey) and without parallel tempering (black). Without parallel tempering, the MCMC chain gets stuck in local minima.

Figure 5