Manpages

The ViennaRNA Package comes with a number of executable programs that provide command line interfaces to the most important algorithms implemented in RNAlib.

Find an overview of these programs and their corresponding manual pages below.

Main Programs

Program	Description
RNA2Dfold	Compute MFE structure, partition function and representative sample structures of k,l neighborhoods
RNAaliduplex	Predict conserved RNA-RNA interactions between two alignments
RNAalifold	Calculate secondary structures for a set of aligned RNA sequences
RNAcofold	Calculate secondary structures of two RNAs with dimerization
RNAdistance	Calculate distances between RNA secondary structures
RNAdos	Calculate the density of states for each energy band of an RNA
RNAduplex	Compute the structure upon hybridization of two RNA strands
RNAeval	Evaluate free energy of RNA sequences with given secondary structure
RNAfold	Calculate minimum free energy secondary structures and partition function of RNAs
RNAheat	Calculate the specific heat (melting curve) of an RNA sequence
RNAinverse	Find RNA sequences with given secondary structure (sequence design)
RNALalifold	Calculate locally stable secondary structures for a set of aligned RNAs
RNALfold	Calculate locally stable secondary structures of long RNAs
RNAmultifold	Compute thermodynamic properties for interaction complexes of multiple RNAs
RNApaln	RNA alignment based on sequence base pairing propensities
RNApdist	Calculate distances between thermodynamic RNA secondary structures ensembles
RNAparconv	Convert energy parameter files from ViennaRNA 1.8 to 2.0 format
RNAPKplex	Predict RNA secondary structures including pseudoknots
RNAplex	Find targets of a query RNA
RNAplfold	Calculate average pair probabilities for locally stable secondary structures
RNAplot	Draw RNA Secondary Structures in PostScript, SVG, or GML
RNApvmin	Calculate a perturbation vector that minimizes discrepancies between predicted and observed pairing probabilities
RNAsnoop	Find targets of a query H/ACA snoRNA
RNAsubopt	Calculate suboptimal secondary structures of RNAs
RNAup	Calculate the thermodynamics of RNA-RNA interactions

Additional Programs

We include the following additional programs in our distribution of the ViennaRNA Package. Whether or not they are installed together with the ViennaRNA Package depends on its Configuration.

Program	Description
AnalyseDists	Analyse a distance matrix
AnalyseSeqs	Analyse a set of sequences of common length
Kinfold	Simulate kinetic folding of RNA secondary structures
kinwalker	Predict RNA folding trajectories
RNAforester	Compare RNA secondary structures via forest alignment
RNAlocmin	Calculate local minima from structures via gradient walks
RNAxplorer	Explore the RNA conformation space through sampling and other techniques