Figure 1.

Example calls of programs included in the ViennaRNA Package and their corresponding output. (A) Single sequence analysis using RNAfold. (B) Locally optimal secondary structures and base pair probabilities using RNAplfold and RNALfold. (C) Interaction thermodynamics of two RNA sequences computed by RNAup. (D) Consensus structures and base pair probabilities for RNA sequence alignments obtained from RNAalifold. (E) Secondary structure of an RNA dimer calculated by RNAcofold. (F) Folding kinetics using RNAsubopt in conjunction with the external programs barriers and treekin. (G) Suboptimal secondary structures generated by RNAsubopt. For a detailed description see the appendix.