SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework
MPD Alignment for the HDV Dataset Consisting of 15 Sequences of HDV Ribozymes
The name of each sequence indicates the NCBI accession number of the strain. The ribozyme contains one pseudoknot and a variable helix as shown in the line above the alignment, which denotes the known reference structure in dot-bracket, or Vienna, notation. The posterior probabilities for each alignment column were derived from the multiple sequence alignments that the MCMC method sampled and are indicated at the top of the figure.