Table 1.
Main features of the interactive programs provided by the ViennaRNA Package 2.0
| Program | Energy model variants | 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 | + | + |
The characters + and - show presence and absence of a certain feature, while NA indicates that the feature is not applicable in a given context. Abbreviations of input file formats are (C)lustal-format, (F)asta-format, (S)tockholm-format, and (V)iennaRNA-format. Support for prediction of suboptimal structures may be implemented as (B)oltzmann weighted sampling, exhaustive (E)numeration of all structures in a given energy band, and (Z)uker-style suboptimal structures. Programs marked by an asterisk (*) were not included in a previous release of the ViennaRNA Package.