SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework (original) (raw)
Figure 1
Alignment Prior
For calculating the gap contribution to the prior, _F_3(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.