From: ViennaRNA Package 2.0
Program | Â | Â | Â | Energy model variants | Â | Â | Data formats | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
 | intramolecular bp | intermolecular bp | structure constraint | canonical structures | circular sequence | dangling end model(s) | centroid structure | MEA structure | suboptimal structures | base pair probabilities/partition function | input format(s) | text output file(s) | PostScript plot(s) |
 |  | single sequence analysis (global variant) |  |  |  |  | |||||||
RNAfold | + | - | + | + | + | 0,1,2,3 | + | + | - | + | F,V | - | + |
RNAsubopt | + | + | + | + | + | 0,1,2,3 | NA | NA | B,E,Z | - | F,V | - | - |
RNAcofold | + | + | + | + | NA | 0,1,2,3 | - | - | - | + | F,V | + | + |
RNAup | + | + | + | + | - | 0,2 | - | - | - | + | V | + | - |
RNAduplex | - | + | - | + | - | 0,1,2,3 | - | - | E | - | V | + | - |
RNA2Dfold* | + | - | - | - | + | 0,2 | - | + | B | - | V | - | - |
RNAPKplex* | + | - | - | + | - | 0,1,2,3 | - | - | E | - | F,V | - | + |
RNAplex* | - | + | + | - | - | 2 | NA | NA | E | - | V,W | + | + |
RNAsnoop* | + | + | + | + | - | 2 | NA | NA | E | - | V,W | + | + |
 |  |  | single sequence analysis (local variant) |  |  |  |  | ||||||
RNALfold | + | - | - | + | - | 0,1,2,3 | - | - | - | - | F,V | - | - |
RNAplfold | + | - | - | + | - | 0,2 | - | - | - | - | F,V | + | + |
 |  |  | comparative analysis (global variant) |  |  |  |  | ||||||
RNAalifold | + | - | + | + | + | 0,2 | + | + | B | + | C,S | - | + |
RNAaliduplex | - | + | - | + | - | 0,1,2,3 | - | - | E | - | C,S | + | + |
 |  |  | comparative analysis (local variant) |  |  |  |  | ||||||
RNALalifold* | + | - | - | + | - | 0,1,2,3 | - | - | - | + | C,S | + | + |
 |  |  |  | Misc. analysis/Utilities |  |  |  |  |  | ||||
RNAeval | + | + | NA | NA | + | 0,1,2,3 | NA | NA | NA | NA | F,V | - | - |
RNAplot | NA | NA | NA | NA | + | NA | NA | NA | NA | NA | F,V | - | + |
RNAheat | + | - | - | + | - | 0,2 | - | - | - | - | F,V | - | - |
RNAinverse | + | - | NA | NA | - | 0,1,2,3 | NA | NA | NA | NA | V | - | - |
RNApaln | + | - | - | + | - | 0,1,2,3 | NA | NA | NA | + | V | + | + |
RNApdist | + | - | - | - | - | 0,1,2,3 | NA | NA | NA | + | V | + | + |
RNAdistance | + | - | NA | NA | NA | NA | NA | NA | NA | NA | V | + | + |