▼ 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 | MFE structures for base pair distance classes |
2Dpfold.h | Partition function implementations for base pair distance classes |
ali_plex.h | |
alifold.h | Functions for comparative structure prediction using 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 implementations for RNA-RNA interaction |
combinatorics.h | Various implementations that deal with combinatorial aspects of RNA/DNA folding |
commands.h | Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation |
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_ligand.h | Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework |
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 | Various data structures and pre-processor macros |
dist_vars.h | Global variables for Distance-Package |
dp_matrices.h | Functions to deal with standard dynamic programming (DP) matrices |
duplex.h | Functions for simple RNA-RNA duplex interactions |
edit_cost.h | Global variables for Edit Costs included by treedist.c and stringdist.c |
energy_const.h | Energy parameter constants |
energy_par.h | |
equilibrium_probs.h | Equilibrium Probability implementations |
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 | Read and write different file formats for RNA sequences, structures |
file_formats_msa.h | Functions dealing with file formats for Multiple Sequence Alignments (MSA) |
file_utils.h | Several utilities for file handling |
findpath.h | A breadth-first search heuristic for optimal direct folding paths |
fold.h | MFE calculations for single RNA sequences |
fold_vars.h | Here all all declarations of the global variables used throughout RNAlib |
gquad.h | G-quadruplexes |
grammar.h | Implementations for the RNA folding grammar |
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 | Functions for locally optimal MFE structure prediction |
loop_energies.h | Energy evaluation for MFE and partition function calculations |
LPfold.h | Partition function implementation for 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 | Functions to deal with sets of energy parameters |
part_func.h | Partition function implementations |
part_func_co.h | Partition function for two RNA sequences |
part_func_up.h | Implementations for accessibility and RNA-RNA interaction as a 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 | Read and write energy parameter files |
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 |
structured_domains.h | This module provides interfaces that deal with additional structured domains in the folding grammar |
subopt.h | RNAsubopt and density of states declarations |
svm_utils.h | |
treedist.h | Functions for Tree Edit Distances |
units.h | Physical Units and Functions to convert them into each other |
unstructured_domains.h | Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches |
utils.h | General utility- and helper-functions used throughout the ViennaRNA Package |