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

Figure 1

Alignment Prior

For calculating the gap contribution to the prior, F3(A), we decompose the alignment into homogeneous groups based only on the pattern of the gaps in the alignment. Each asterisk represents a nucleotide in the alignment, and each dash denotes a gap in the alignment.

Figure 1