Which programs are available?

RNA2Dfold	Compute coarse grained energy landscape of representative sample structures
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
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
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 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 and markup RNA secondary structures in PostScript, SVG, or GML
RNAsnoop	Find targets of a query H/ACA snoRNA
RNAsubopt	Calculate suboptimal secondary structures of RNAs
RNAup	Calculate the thermodynamics of RNA-RNA interactions
Kinfold	simulates the stochastic folding kinetics of RNA sequences into secondary structures
RNAforester 1	compare RNA secondary structures via forest alignment