SimulFold 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.

Input Multiple Sequence Alignment

Paste a multiple sequence alignment of one or more sequences in FASTA format (up to 20kb total). Click for example

Note that filename reserved characters (i.e. nearly anything that's not alphanumeric) in the FASTA headers will be replaced with underscores.
MISSING INPUT: Please paste of upload input data.
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(Optional) Phylogenetic Tree

Paste a phylogeny tree in Newick format. All species must match those in both alignments. Click for example

One will be computed if no tree is given (and can be retrieved in the results tar-ball).
MISSING INPUT: Please paste of upload input data.
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Sampling Options

Choose the properties that SimulFold is allowed to optimize (and compute probabilities for):

Structure
Alignment
Tree
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