File List
Here is a list of all documented files with brief descriptions:

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