Modules
Here is a list of all modules:

RNA Secondary Structure Prediction | This module contains all functions related to thermodynamic folding of RNAs
Computing Minimum Free Energy (MFE) Structures | This section covers all functions and variables related to the calculation of minimum free energy (MFE) structures
MFE Structures of single Nucleic Acid Sequences | This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences
MFE Structures of two hybridized Sequences |
MFE Consensus Structures for Sequence Alignment(s) |
Local MFE structure Prediction and Z-scores |
Calculating MFE representatives of a Distance Based Partitioning | Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures
Computing Partition Functions and Pair Probabilities | This section provides information about all functions and variables related to the calculation of the partition function and base pair probabilities
Compute the structure with maximum expected accuracy (MEA) |
Compute the centroid structure |
Partition Function for two hybridized Sequences | Partition Function Cofolding
Partition Function for two hybridized Sequences as a stepwise Process | Partition Function Cofolding as a stepwise process
Partition Function and Base Pair Probabilities for Sequence Alignment(s) |
Partition functions for locally stable secondary structures |
Calculate Partition Functions of a Distance Based Partitioning | Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures
Enumerating Suboptimal Structures |
Suboptimal structures according to Zuker et al. 1989 |
Suboptimal structures within an energy band arround the MFE |
Stochastic backtracking in the Ensemble |
Stochastic Backtracking of Consensus Structures from Sequence Alignment(s) |
Stochastic Backtracking of Structures from Distance Based Partitioning | Contains functions related to stochastic backtracking from a specified distance class
Calculate Secondary Structures of two RNAs upon Dimerization | Predict structures formed by two molecules upon hybridization
MFE Structures of two hybridized Sequences |
Partition Function for two hybridized Sequences | Partition Function Cofolding
Partition Function for two hybridized Sequences as a stepwise Process | Partition Function Cofolding as a stepwise process
Predicting Consensus Structures from Alignment(s) | Compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
MFE Consensus Structures for Sequence Alignment(s) |
Partition Function and Base Pair Probabilities for Sequence Alignment(s) |
Stochastic Backtracking of Consensus Structures from Sequence Alignment(s) |
Local MFE consensus structures for Sequence Alignments |
Predicting Locally stable structures of large sequences |
Local MFE structure Prediction and Z-scores |
Partition functions for locally stable secondary structures |
Local MFE consensus structures for Sequence Alignments |
Classified Dynamic Programming |
Distance based partitioning of the Secondary Structure Space | Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space
Calculating MFE representatives of a Distance Based Partitioning | Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures
Calculate Partition Functions of a Distance Based Partitioning | Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures
Stochastic Backtracking of Structures from Distance Based Partitioning | Contains functions related to stochastic backtracking from a specified distance class
Compute the Density of States |
Inverse Secondary Structure Prediction |
Refolding paths between secondary structues |
Direct refolding paths between two secondary structures | Implementation of heuristics to explore optimal (re-)folding paths between two secondary structures
Free Energy Evaluation for given Sequence / Structure Pairs | This module contains all functions and variables related to energy evaluation of sequence/structure pairs
Processing and Evaluating Decomposed Loops |
Energy Parameter Sets and Boltzmann Factors | All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s)
Reading/Writing Energy Parameter Sets from/to File | Read and Write energy parameter sets from and to text files
Converting Energy Parameter Files | Convert energy parameter files into the latest format
Manipulation of the Prediction Models |
Constraining the Secondary Structure Predictions and Evaluations | This module covers all functions and variables related to the problem of incorporating secondary structure constraints into the folding recursions
Hard Constraints | This module covers all functionality for hard constraints in secondary structure prediction
Soft Constraints | Functions and data structures for secondary structure soft constraints
Incorporating SHAPE reactivity data | Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints
Incorporating ligands binding to specific sequence/structure motifs | This module covers functions that enable the incorporation of ligand binding free energies to specific hairpin/interior loop motifs by means of generic soft constraints
Generate soft constraints from data | Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments
Data Structures and Preprocessor Macros | Most datastructures and typedefs shared among the ViennaRNA Package can be found here
The Fold Compound | This module provides interfaces that deal with the most basic data structure used in structure predicting and energy evaluating function of the RNAlib
The Dynamic Programming Matrices | This module provides interfaces that deal with creation and destruction of dynamic programming matrices used within the RNAlib
Utilities |
Parsing, Converting, and Comparing - Functions to Manipulate Sequence and Structure Strings |
Parsing, Converting, and Comparing - Functions to Manipulate Secondary Structures |
Various utilities for Sequence Alignments, and Comparative Structure Prediction |
Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments |
Functions for Creating RNA Secondary Structures Plots, Dot-Plots, and More |