ViennaRNA Directory Reference
Directory dependency graph for ViennaRNA:

## Files

file | 1.8.4_epars.h [code]
| Free energy parameters for parameter file conversion.
file | 1.8.4_intloops.h [code]
| Free energy parameters for interior loop contributions needed by the parameter file conversion functions.
file | 2Dfold.h [code]
file | 2Dpfold.h [code]
file | ali_plex.h [code]
file | alifold.h [code]
| compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
file | aln_util.h [code]
| Various utility- and helper-functions for sequence alignments and comparative structure prediction.
file | alphabet.h [code]
| Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets.
file | boltzmann_sampling.h [code]
| Boltzmann Sampling of secondary structures from the ensemble.
file | centroid.h [code]
| Centroid structure computation.
file | cofold.h [code]
| MFE version of cofolding routines.
file | constraints.h [code]
| Functions and data structures for constraining secondary structure predictions and evaluation.
file | constraints_hard.h [code]
| Functions and data structures for handling of secondary structure hard constraints.
file | constraints_SHAPE.h [code]
| This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints.
file | constraints_soft.h [code]
| Functions and data structures for secondary structure soft constraints.
file | convert_epars.h [code]
| Functions and definitions for energy parameter file format conversion.
file | data_structures.h [code]
file | dist_vars.h [code]
| Global variables for Distance-Package.
file | dp_matrices.h [code]
file | duplex.h [code]
| Duplex folding function declarations...
file | edit_cost.h [code]
| global variables for Edit Costs included by treedist.c and stringdist.c
file | energy_const.h [code]
file | energy_par.h [code]
file | eval.h [code]
| Functions and variables related to energy evaluation of sequence/structure pairs.
file | exterior_loops.h [code]
| Energy evaluation of exterior loops for MFE and partition function calculations.
file | file_formats.h [code]
| Functions dealing with file formats for RNA sequences, structures, and alignments.
file | findpath.h [code]
file | fold.h [code]
| MFE calculations for single RNA sequences.
file | fold_vars.h [code]
| Here all all declarations of the global variables used throughout RNAlib.
file | gquad.h [code]
| Various functions related to G-quadruplex computations.
file | hairpin_loops.h [code]
| Energy evaluation of hairpin loops for MFE and partition function calculations.
file | interior_loops.h [code]
| Energy evaluation of interior loops for MFE and partition function calculations.
file | intl11.h [code]
file | intl11dH.h [code]
file | intl21.h [code]
file | intl21dH.h [code]
file | intl22.h [code]
file | intl22dH.h [code]
file | inverse.h [code]
| Inverse folding routines.
file | Lfold.h [code]
| Predicting local MFE structures of large sequences.
file | ligand.h [code]
| Functions for incorporation of ligands binding to haipirn and interior loop motifs.
file | list.h [code]
file | loop_energies.h [code]
| Energy evaluation for MFE and partition function calculations.
file | LPfold.h [code]
| Function declarations of partition function variants of the Lfold algorithm.
file | MEA.h [code]
| Computes a MEA (maximum expected accuracy) structure.
file | mfe.h [code]
| MFE calculations for single RNA sequences.
file | mm.h [code]
| Several Maximum Matching implementations.
file | model.h [code]
| The model details data structure and its corresponding modifiers.
file | move_set.h [code]
file | multibranch_loops.h [code]
| Energy evaluation of multibranch loops for MFE and partition function calculations.
file | naview.h [code]
file | pair_mat.h [code]
file | params.h [code]
file | part_func.h [code]
| Partition function of single RNA sequences.
file | part_func_co.h [code]
| Partition function for two RNA sequences.
file | part_func_up.h [code]
| Partition Function Cofolding as stepwise process.
file | perturbation_fold.h [code]
| Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments.
file | PKplex.h [code]
file | plex.h [code]
file | plot_aln.h [code]
| Various functions for plotting Sequence / Structure Alignments.
file | plot_layouts.h [code]
| Secondary structure plot layout algorithms.
file | plot_structure.h [code]
| Various functions for plotting RNA secondary structures.
file | ProfileAln.h [code]
file | profiledist.h [code]
file | PS_dot.h [code]
| Various functions for plotting RNA secondary structures, dot-plots and other visualizations.
file | read_epars.h [code]
file | ribo.h [code]
| Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.
file | RNAstruct.h [code]
| Parsing and Coarse Graining of Structures.
file | snofold.h [code]
file | snoop.h [code]
file | string_utils.h [code]
| General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package.
file | stringdist.h [code]
| Functions for String Alignment.
file | structure_utils.h [code]
| Various utility- and helper-functions for secondary structure parsing, converting, etc.
file | subopt.h [code]
| RNAsubopt and density of states declarations.
file | svm_utils.h [code]
file | treedist.h [code]
| Functions for Tree Edit Distances.
file | utils.h [code]
| General utility- and helper-functions used throughout the ViennaRNA Package.