Carnac : software for analyzing the hypothetical secondary structure of a family of homologous RNA, predicting if there is a shared secondary structure, and predicting the folded stems in it. The input is a set of single-stranded RNA sequences that need not to be aligned. A thermodynamic model with energy minimization combined with locally conserved primary structure and sequence covariations is used.
CMFinder : software for RNA motif prediction based on an expectation maximization algorithm using covariance models for motif description, heuristics for motif search, and a Bayesian framework for structure prediction that combines folding energy and sequence covariation.
ComRNA : software for predicting common RNA secondary structure motifs in a group of related sequences. The algorithm applies graph theory to automatically detect common RNA secondary structure motifs in a group of functionally or evolutionarily related RNA sequences. It does not require global sequence similarities or prior structural alignment, and is able to detect pseudoknot structures.
CONTRA : CONTRA (CONditional TRAining for biosequence analysis) is a software project that applies discriminatively-trained probabilistic models (conditional random fields and their variants) to sequence labeling problems in bioinformatics. Software distributed through this project includes: CONTRAlign, a protein sequence aligner; CONTRAfold, an RNA secondary structure folder; and CONTRAST, a multiple sequence de novo gene predictor
DINAMelt : Collection of software targeted to computing secondary structure, folding, hybridization, and free energies for DNA or RNA sequences.
Dynalign : software that improves accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity.
FoldAlign : software for local simultaneous folding and aligning of two or more RNA sequences.
Gibbs Recursive Sampler : software package for locating common elements, such as motifs and conserved regions, in nucleic acid or protein sequences based on site sampling, motif sampling and recursive sampling.
MC-Fold : software from the Francois Major lab at University of Montreal that predicts RNA secondary based on non-canonical base pairs and nucleotide cyclic motifs using sequence as input.
Mfold : the well-known software from the Zuker lab at RPI that predicts RNA secondary structure using sequence as input (related: see DINAMelt above, also from the Zuker lab at RPI).
Pfold : software that takes an alignment of RNA sequences as input and predicts a common structure for all sequences.
RNAalifold : software that predicts the consensus structure of a set aligned RNA sequences by taking into account both thermodynamic stability and sequence covariation.
RnamlView : Java software that allows dynamic graphical viewing of RNA secondary structures. It can open a rnaml format file and display its directory tree representation and the secondary structure stored in it and allows the user to dynamically manipulate and annotate the displayed RNA secondary structure.
RNAstructure : software that predicts RNA/DNA secondary structure and performs additional analysis. Includes a secondary structure prediction algorithm, a partition function algorithm for predicting base pairing probabilities, Dynalign for finding a structure common to multiple sequences, efn2 for predicting the stability of a secondary strcuture, OligoWalk for predicting binding affinity to an RNA target, and OligoScreen for predicting the unimolecular and bimolecular self structure for a large number of sequences.
RSAT : Regulatory Sequence Analysis Tools (RSAT) provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences through non-structural pattern discovery across multiple sequences.
S2S : Sequence to Structure (S2S) is a Java-based software that provides a framework for display, manipulation, and integration of varied data such as multiple sequence alignments, secondary structure, and tertiary structure for RNA.
SAFA : Semi Automated Footprinting Analysis (SAFA) software for quantitatively analyzing chemical footprinting gels that provide insights into 3D RNA structure.
SCARNA : software for structural alignment of a pair of RNA sequences and calculation of their similarities based on the estimated common secondary structures.
Sfold : software that uses statistical tools to predict RNA secondary structure, assess RNA target accessibility, and carry out rational design of RNA-targeting nucleic acids.