RNAlib-2.2.7
ViennaRNA Directory Reference
+ Directory dependency graph for ViennaRNA:

Files

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