ViennaRNA Package 2 - Man Pages

Although the man pages are also included in the ViennaRNA Package itself it is sometime useful to have an HTML translation making them accessible through a web browser.

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

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 2.0 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

RNAsnoop
Find targets of a query H/ACA snoRNA

RNAsubopt
Calculate suboptimal secondary structures of RNAs

RNAup
Calculate the thermodynamics of RNA-RNA interactions