SimulFold 1.0 is a computer program for co-estimating an RNA structure including pseudo-knots, a multiple-sequence alignment and an evolutionary tree, given a set of evolutionarily related RNA sequences as input. In other words, you give SimulFold an initial alignment of RNA sequences as input and it will predict a consensus RNA structure which may include pseudo-knots while simultaneously estimating the sequence alignment and the evolutionary tree relating the RNA sequences. This means, in particular, that the input alignment need not be a manually curated alignment of high quality. SimulFold employs a Markov Chain Monte Carlo in order to sample from the joint posterior distribution of RNA structures, alignments and trees. A post-processing step is then used to cluster the sampled RNA structures into one RNA structure.

SimulFold paper and software:

• SimulFold paper citation: Irmtraud M. Meyer and I. Miklos, SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Tress Using a Bayesian MCMC Framework, PLoS Computational Biology (2007) 3(8): e149
• SimulFold tar-ball (see included COPYRIGHT file)
• use "java SimulFold alignment_file tree_file -S -T -A" to execute the program locally and to sample alignments (A), trees (T) and structures (S)
• please note that input trees on the command line have to be binary, rooted trees in Newick format
• bp2bistruc tar-ball

• CARNAC input and output files (tar-ball)
• HXMATCH input and output files (tar-ball)
• Pfold input and output files (tar-ball)
• RNAalifold input and output files (tar-ball)
• SimulFold input and output files (tar-ball)
• SimulFold raw output files (LARGE tar-ball 4.5MB)