RNAlib-2.2.1
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
 boltzmann_sampling.hBoltzmann Sampling of secondary structures from the ensemble
 centroid.hCentroid structure computation
 cofold.hMFE version of cofolding routines
 constraints.h
 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.h
 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.h
 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