Related tools
RNAdos
RNAdos calculates density-of-states summaries for RNA sequences, reporting representative structures and state counts across energy bands.
RNAeval
RNAeval calculates the free energy of an RNA secondary structure for a given sequence. Evaluates if a proposed structure is thermodynamically favorable.
RNAfold
RNAfold predicts RNA secondary structure using minimum free energy (MFE) algorithms and optionally returns partition-function ensemble metrics when explicitly enabled.
RNALfold
RNALfold reports locally stable RNA secondary structures within a sliding window and returns their start and end positions on the input sequence.
RNAplfold
RNAplfold computes local base pair probabilities using a sliding window approach. Useful for analyzing accessibility and identifying binding sites in long RNA sequences.
RNAsubopt
RNAsubopt enumerates all RNA secondary structures within a specified energy range above the minimum free energy (MFE). Useful for exploring the structural ensemble and identifying alternative conformations.
RNAcofold
RNAcofold predicts the joint secondary structure of two interacting RNA molecules and optionally reports partition-function and concentration-dependent equilibrium metrics.
RNAdistance
RNAdistance compares RNA secondary structures using the selected native ViennaRNA distance representation and comparison mode.
RNAduplex
RNAduplex computes the hybridization structure between two RNA sequences. Predicts the optimal duplex formation and binding energy.
RNAplex
RNAplex predicts fast query-target RNA interactions, reporting parsed hit coordinates, structures, and energies.