# 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