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| 2Dfold.h |
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| 2Dpfold.h |
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| ali_plex.h |
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| alifold.h |
| compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
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| aln_util.h |
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| cofold.h |
| MFE version of cofolding routines.
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| convert_epars.h |
| Functions and definitions for energy parameter file format conversion.
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| data_structures.h |
| All datastructures and typedefs shared among the Vienna RNA Package can be found here.
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| dist_vars.h |
| Global variables for Distance-Package.
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| duplex.h |
| Duplex folding function declarations...
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| edit_cost.h |
| global variables for Edit Costs included by treedist.c and stringdist.c
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| energy_const.h |
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| energy_par.h |
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| energy_par_D.h |
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| energy_par_RD.h |
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| findpath.h |
| Compute direct refolding paths between two secondary structures.
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| fold.h |
| MFE calculations and energy evaluations for single RNA sequences.
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| fold_vars.h |
| Here all all declarations of the global variables used throughout RNAlib.
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| gquad.h |
| Various functions related to G-quadruplex computations.
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| inverse.h |
| Inverse folding routines.
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| Lfold.h |
| Predicting local MFE structures of large sequences.
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| loop_energies.h |
| Energy evaluation for MFE and partition function calculations.
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| LPfold.h |
| Function declarations of partition function variants of the Lfold algorithm.
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| MEA.h |
| Computes a MEA (maximum expected accuracy) structure.
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| mm.h |
| Several Maximum Matching implementations.
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| move_set.h |
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| naview.h |
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| pair_mat.h |
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| params.h |
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| part_func.h |
| Partition function of single RNA sequences.
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| part_func_co.h |
| Partition function for two RNA sequences.
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| part_func_up.h |
| Partition Function Cofolding as stepwise process.
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| PKplex.h |
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| plex.h |
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| plot_layouts.h |
| Secondary structure plot layout algorithms.
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| ProfileAln.h |
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| profiledist.h |
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| PS_dot.h |
| Various functions for plotting RNA secondary structures, dot-plots and other visualizations.
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| read_epars.h |
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| ribo.h |
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| RNAstruct.h |
| Parsing and Coarse Graining of Structures.
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| snofold.h |
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| snoop.h |
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| stringdist.h |
| Functions for String Alignment.
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| subopt.h |
| RNAsubopt and density of states declarations.
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| svm_utils.h |
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| treedist.h |
| Functions for Tree Edit Distances.
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| utils.h |
| Various utility- and helper-functions used throughout the Vienna RNA package.
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