From: 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 | + | + |