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. | |