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 

Compute MFE structure, partition function and representative sample structures of k,l neighborhoods 

Predict conserved RNARNA interactions between two alignments 

Calculate secondary structures for a set of aligned RNA sequences 

Calculate secondary structures of two RNAs with dimerization 

Calculate distances between RNA secondary structures 

Calculate the density of states for each energy band of an RNA 

Compute the structure upon hybridization of two RNA strands 

Evaluate free energy of RNA sequences with given secondary structure 

Calculate minimum free energy secondary structures and partition function of RNAs 

Calculate the specific heat (melting curve) of an RNA sequence 

Find RNA sequences with given secondary structure (sequence design) 

Calculate locally stable secondary structures for a set of aligned RNAs 

Calculate locally stable secondary structures of long RNAs 

Compute thermodynamic properties for interaction complexes of multiple RNAs 

RNA alignment based on sequence base pairing propensities 

Calculate distances between thermodynamic RNA secondary structures ensembles 

Convert energy parameter files from ViennaRNA 1.8 to 2.0 format 

Predict RNA secondary structures including pseudoknots 

Find targets of a query RNA 

Calculate average pair probabilities for locally stable secondary structures 

Draw RNA Secondary Structures in PostScript, SVG, or GML 

Calculate a perturbation vector that minimizes discrepancies between predicted and observed pairing probabilities 

Find targets of a query H/ACA snoRNA 

Calculate suboptimal secondary structures of RNAs 

Calculate the thermodynamics of RNARNA 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 