RNAlib-2.2.7
File List
Here is a list of all documented files with brief descriptions:
[detail level 12]
  ViennaRNA
 1.8.4_epars.hFree energy parameters for parameter file conversion
 1.8.4_intloops.hFree energy parameters for interior loop contributions needed by the parameter file conversion functions
 2Dfold.h
 2Dpfold.h
 ali_plex.h
 alifold.hCompute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
 aln_util.hVarious utility- and helper-functions for sequence alignments and comparative structure prediction
 alphabet.hFunctions to process, convert, and generally handle different nucleotide and/or base pair alphabets
 boltzmann_sampling.hBoltzmann Sampling of secondary structures from the ensemble
 centroid.hCentroid structure computation
 cofold.hMFE version of cofolding routines
 constraints.hFunctions and data structures for constraining secondary structure predictions and evaluation
 constraints_hard.hFunctions and data structures for handling of secondary structure hard constraints
 constraints_SHAPE.hThis module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints
 constraints_soft.hFunctions and data structures for secondary structure soft constraints
 convert_epars.hFunctions and definitions for energy parameter file format conversion
 data_structures.h
 dist_vars.hGlobal variables for Distance-Package
 dp_matrices.h
 duplex.hDuplex folding function declarations..
 edit_cost.hGlobal variables for Edit Costs included by treedist.c and stringdist.c
 energy_const.h
 energy_par.h
 eval.hFunctions and variables related to energy evaluation of sequence/structure pairs
 exterior_loops.hEnergy evaluation of exterior loops for MFE and partition function calculations
 file_formats.hFunctions dealing with file formats for RNA sequences, structures, and alignments
 findpath.h
 fold.hMFE calculations for single RNA sequences
 fold_vars.hHere all all declarations of the global variables used throughout RNAlib
 gquad.hVarious functions related to G-quadruplex computations
 hairpin_loops.hEnergy evaluation of hairpin loops for MFE and partition function calculations
 interior_loops.hEnergy evaluation of interior loops for MFE and partition function calculations
 intl11.h
 intl11dH.h
 intl21.h
 intl21dH.h
 intl22.h
 intl22dH.h
 inverse.hInverse folding routines
 Lfold.hPredicting local MFE structures of large sequences
 ligand.hFunctions for incorporation of ligands binding to haipirn and interior loop motifs
 list.h
 loop_energies.hEnergy evaluation for MFE and partition function calculations
 LPfold.hFunction declarations of partition function variants of the Lfold algorithm
 MEA.hComputes a MEA (maximum expected accuracy) structure
 mfe.hMFE calculations for single RNA sequences
 mm.hSeveral Maximum Matching implementations
 model.hThe model details data structure and its corresponding modifiers
 move_set.h
 multibranch_loops.hEnergy evaluation of multibranch loops for MFE and partition function calculations
 naview.h
 pair_mat.h
 params.h
 part_func.hPartition function of single RNA sequences
 part_func_co.hPartition function for two RNA sequences
 part_func_up.hPartition Function Cofolding as stepwise process
 perturbation_fold.hFind 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.hVarious functions for plotting Sequence / Structure Alignments
 plot_layouts.hSecondary structure plot layout algorithms
 plot_structure.hVarious functions for plotting RNA secondary structures
 ProfileAln.h
 profiledist.h
 PS_dot.hVarious functions for plotting RNA secondary structures, dot-plots and other visualizations
 read_epars.h
 ribo.hParse RiboSum Scoring Matrices for Covariance Scoring of Alignments
 RNAstruct.hParsing and Coarse Graining of Structures
 snofold.h
 snoop.h
 string_utils.hGeneral utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package
 stringdist.hFunctions for String Alignment
 structure_utils.hVarious utility- and helper-functions for secondary structure parsing, converting, etc
 subopt.hRNAsubopt and density of states declarations
 svm_utils.h
 treedist.hFunctions for Tree Edit Distances
 utils.hGeneral utility- and helper-functions used throughout the ViennaRNA Package