► 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 [24] |
RNAturtle.h | Implementation of the RNAturtle RNA secondary structure layout algorithm [24] |
alignments.h | Various functions for plotting Sequence / Structure Alignments |
layouts.h | Secondary structure plot layout algorithms |
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/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 |
pf_multifold.h | |
pk_plex.h | Heuristics for two-step pseudoknot forming interaction predictions |
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 |
subopt_zuker.h | |
svm_utils.h | Use ViennaRNA/utils/svm.h instead |
treedist.h | Functions for Tree Edit Distances |
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 |
wrap_dlib.h | |
zscore.h | |