| ► ViennaRNA | |
| ► constraints | |
| basic.h | Functions and data structures for constraining secondary structure predictions and evaluation |
| hard.h | Functions and data structures for handling of secondary structure hard constraints |
| ligand.h | Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework |
| SHAPE.h | This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints |
| soft.h | Functions and data structures for secondary structure soft constraints |
| ► datastructures | |
| basic.h | Various data structures and pre-processor macros |
| char_stream.h | Implementation of a dynamic, buffered character stream |
| hash_tables.h | Implementations of hash table functions |
| heap.h | Implementation of an abstract heap data structure |
| lists.h | |
| stream_output.h | An implementation of a buffered, ordered stream output data structure |
| ► io | |
| 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) |
| utils.h | Several utilities for file handling |
| ► landscape | |
| findpath.h | A breadth-first search heuristic for optimal direct folding paths |
| move.h | Methods to operate with structural neighbors of RNA secondary structures |
| neighbor.h | Methods to compute the neighbors of an RNA secondary structure |
| paths.h | API for computing (optimal) (re-)folding paths between secondary structures |
| walk.h | Methods to generate particular paths such as gradient or random walks through the energy landscape of an RNA sequence |
| ► loops | |
| all.h | Energy evaluation for MFE and partition function calculations |
| external.h | Energy evaluation of exterior loops for MFE and partition function calculations |
| hairpin.h | Energy evaluation of hairpin loops for MFE and partition function calculations |
| internal.h | Energy evaluation of interior loops for MFE and partition function calculations |
| multibranch.h | Energy evaluation of multibranch loops for MFE and partition function calculations |
| ► params | |
| 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 |
| basic.h | Functions to deal with sets of energy parameters |
| constants.h | Energy parameter constants |
| convert.h | Functions and definitions for energy parameter file format conversion |
| default.h | |
| intl11.h | |
| intl11dH.h | |
| intl21.h | |
| intl21dH.h | |
| intl22.h | |
| intl22dH.h | |
| io.h | Read and write energy parameter files |
| ► plotting | |
| ► RNApuzzler | |
| RNApuzzler.h | Implementation of the RNApuzzler RNA secondary structure layout algorithm [23] |
| RNAturtle.h | Implementation of the RNAturtle RNA secondary structure layout algorithm [23] |
| alignments.h | Various functions for plotting Sequence / Structure Alignments |
| layouts.h | Secondary structure plot layout algorithms |
| naview.h | Implementation of the Naview RNA secondary structure layout algorithm [5] |
| probabilities.h | Various functions for plotting RNA secondary structures, dot-plots and other visualizations |
| structures.h | Various functions for plotting RNA secondary structures |
| utils.h | Various utilities to assist in plotting secondary structures and consensus structures |
| ► search | |
| BoyerMoore.h | Variants of the Boyer-Moore string search algorithm |
| ► utils | |
| alignments.h | Various utility- and helper-functions for sequence alignments and comparative structure prediction |
| basic.h | General utility- and helper-functions used throughout the ViennaRNA Package |
| cpu.h | |
| higher_order_functions.h | |
| strings.h | General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package |
| structures.h | Various utility- and helper-functions for secondary structure parsing, converting, etc |
| svm.h | |
| units.h | Physical Units and Functions to convert them into each other |
| 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 | Use ViennaRNA/utils/alignments.h instead |
| 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 |
| char_stream.h | Use ViennaRNA/datastructures/char_stream.h instead |
| cofold.h | MFE implementations for RNA-RNA interaction |
| combinatorics.h | Various implementations that deal with combinatorial aspects of objects |
| commands.h | Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation |
| concentrations.h | Concentration computations for RNA-RNA interactions |
| constraints.h | Use ViennaRNA/constraints/basic.h instead |
| constraints_hard.h | Use ViennaRNA/constraints/hard.h instead |
| constraints_ligand.h | Use ViennaRNA/constraints/ligand.h instead |
| constraints_SHAPE.h | Use ViennaRNA/constraints/SHAPE.h instead |
| constraints_soft.h | Use ViennaRNA/constraints/soft.h instead |
| convert_epars.h | Use ViennaRNA/params/convert.h instead |
| data_structures.h | Use ViennaRNA/datastructures/basic.h instead |
| 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 | Use ViennaRNA/params/constants.h instead |
| energy_par.h | Use ViennaRNA/params/default.h instead |
| equilibrium_probs.h | Equilibrium Probability implementations |
| eval.h | Functions and variables related to energy evaluation of sequence/structure pairs |
| exterior_loops.h | Use ViennaRNA/loops/external.h instead |
| file_formats.h | Use ViennaRNA/io/file_formats.h instead |
| file_formats_msa.h | Use ViennaRNA/io/file_formats_msa.h instead |
| file_utils.h | Use ViennaRNA/io/utils.h instead |
| findpath.h | Use ViennaRNA/landscape/findpath.h instead |
| fold.h | MFE calculations for single RNA sequences |
| fold_compound.h | The Basic Fold Compound API |
| 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 | Use ViennaRNA/loops/hairpin.h instead |
| heat_capacity.h | Compute heat capacity for an RNA |
| interior_loops.h | Use ViennaRNA/loops/internal.h instead |
| inverse.h | Inverse folding routines |
| Lfold.h | Functions for locally optimal MFE structure prediction |
| loop_energies.h | Use ViennaRNA/loops/all.h instead |
| LPfold.h | Partition function and equilibrium probability implementation for the sliding window algorithm |
| MEA.h | Computes a MEA (maximum expected accuracy) structure |
| mfe.h | Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence data |
| mfe_window.h | Compute local Minimum Free Energy (MFE) using a sliding window approach and backtrace corresponding secondary structures |
| mm.h | Several Maximum Matching implementations |
| model.h | The model details data structure and its corresponding modifiers |
| move_set.h | |
| multibranch_loops.h | Use ViennaRNA/loops/multibranch.h instead |
| naview.h | Use ViennaRNA/plotting/naview.h instead |
| neighbor.h | Use ViennaRNA/landscape/neighbor.h instead |
| pair_mat.h | |
| params.h | Use ViennaRNA/params/basic.h instead |
| 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 |
| part_func_window.h | Partition function and equilibrium probability implementation for the sliding window algorithm |
| 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 | Use ViennaRNA/plotting/alignments.h instead |
| plot_layouts.h | Use ViennaRNA/plotting/layouts.h instead |
| plot_structure.h | Use ViennaRNA/plotting/structures.h instead |
| plot_utils.h | Use ViennaRNA/plotting/utils.h instead |
| ProfileAln.h | |
| profiledist.h | |
| PS_dot.h | Use ViennaRNA/plotting/probabilities.h instead |
| read_epars.h | Use ViennaRNA/params/io.h instead |
| ribo.h | Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments |
| RNAstruct.h | Parsing and Coarse Graining of Structures |
| sequence.h | Functions and data structures related to sequence representations , |
| snofold.h | |
| snoop.h | |
| special_const.h | |
| stream_output.h | Use ViennaRNA/datastructures/stream_output.h instead |
| string_utils.h | Use ViennaRNA/utils/strings.h instead |
| stringdist.h | Functions for String Alignment |
| structure_utils.h | Use ViennaRNA/utils/structures.h instead |
| 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 | Use ViennaRNA/utils/svm.h instead |
| treedist.h | Functions for Tree Edit Distances |
| ugly_bt.h | |
| units.h | Use ViennaRNA/utils/units.h instead |
| unstructured_domains.h | Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches |
| utils.h | Use ViennaRNA/utils/basic.h instead |
| vrna_config.h | |
| walk.h | Use ViennaRNA/landscape/walk.h instead |
| zscore.h | |