ViennaRNA Package 2.0

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.