| ▼ 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 | |
| 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 | Functions dealing with file formats for RNA sequences, and structures |
| file_formats_msa.h | Functions dealing with file formats for Multiple Sequence Alignments (MSA) |
| 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 |
| 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 |