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RNAlib-2.2.9
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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 | 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 | equilibrium_probs.h [code] |
| Equilibrium Probability implementations. | |
| 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, and structures. | |
| file | file_formats_msa.h [code] |
| Functions dealing with file formats for Multiple Sequence Alignments (MSA) | |
| 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 | 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 | 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 | multibranch_loops.h [code] |
| Energy evaluation of multibranch loops for MFE and partition function calculations. | |
| file | naview.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 | 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 | 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 | 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 | treedist.h [code] |
| Functions for Tree Edit Distances. | |
| file | utils.h [code] |
| General utility- and helper-functions used throughout the ViennaRNA Package. | |