Modules
Here is a list of all modules:

RNA Secondary Structure Folding | This module contains all functions related to thermodynamic folding of RNAs
Calculating Minimum Free Energy (MFE) Structures | 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
Calculating 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 |
Change and Precalculate 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
Energy evaluation | This module contains all functions and variables related to energy evaluation of sequence/structure pairs
Searching Sequences for Predefined Structures |
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 |
Parsing and Comparing - Functions to Manipulate Structures |