AUTHORS
CHANGELOG.md
COPYING
MANIFEST.in
NEWS
README.md
config.h
pyproject.toml
setup.cfg
setup.py
ViennaRNA.egg-info/PKG-INFO
ViennaRNA.egg-info/SOURCES.txt
ViennaRNA.egg-info/dependency_links.txt
ViennaRNA.egg-info/top_level.txt
interfaces/Python/RNA_wrap.cpp
interfaces/Python/RNA/RNA.py
interfaces/Python/RNA/__init__.py
interfaces/Python/ViennaRNA/__init__.py
src/ViennaRNA/2Dfold.c
src/ViennaRNA/2Dfold.h
src/ViennaRNA/2Dpfold.c
src/ViennaRNA/2Dpfold.h
src/ViennaRNA/LPfold.h
src/ViennaRNA/Lfold.h
src/ViennaRNA/MEA.h
src/ViennaRNA/PKplex.h
src/ViennaRNA/PS_dot.h
src/ViennaRNA/ProfileAln.c
src/ViennaRNA/ProfileAln.h
src/ViennaRNA/ProfileDist.c
src/ViennaRNA/RNAstruct.c
src/ViennaRNA/RNAstruct.h
src/ViennaRNA/ali_plex.c
src/ViennaRNA/ali_plex.h
src/ViennaRNA/alifold.h
src/ViennaRNA/aln_util.h
src/ViennaRNA/alphabet.h
src/ViennaRNA/boltzmann_sampling.h
src/ViennaRNA/c_plex.c
src/ViennaRNA/centroid.h
src/ViennaRNA/char_stream.h
src/ViennaRNA/cofold.h
src/ViennaRNA/combinatorics.h
src/ViennaRNA/commands.h
src/ViennaRNA/concentrations.c
src/ViennaRNA/concentrations.h
src/ViennaRNA/constraints.h
src/ViennaRNA/constraints_SHAPE.h
src/ViennaRNA/constraints_hard.h
src/ViennaRNA/constraints_ligand.h
src/ViennaRNA/constraints_soft.h
src/ViennaRNA/convert_epars.h
src/ViennaRNA/data_structures.h
src/ViennaRNA/dist_vars.c
src/ViennaRNA/dist_vars.h
src/ViennaRNA/dp_matrices.h
src/ViennaRNA/duplex.c
src/ViennaRNA/duplex.h
src/ViennaRNA/edit_cost.h
src/ViennaRNA/energy_const.h
src/ViennaRNA/energy_par.h
src/ViennaRNA/equilibrium_probs.h
src/ViennaRNA/eval.h
src/ViennaRNA/exterior_loops.h
src/ViennaRNA/file_formats.h
src/ViennaRNA/file_formats_msa.h
src/ViennaRNA/file_utils.h
src/ViennaRNA/findpath.h
src/ViennaRNA/fold.h
src/ViennaRNA/fold_compound.c
src/ViennaRNA/fold_compound.h
src/ViennaRNA/fold_vars.h
src/ViennaRNA/gquad.h
src/ViennaRNA/grammar.h
src/ViennaRNA/hairpin_loops.h
src/ViennaRNA/heat_capacity.c
src/ViennaRNA/heat_capacity.h
src/ViennaRNA/interior_loops.h
src/ViennaRNA/inverse.h
src/ViennaRNA/list.h
src/ViennaRNA/loop_energies.h
src/ViennaRNA/mfe.h
src/ViennaRNA/mfe_window.h
src/ViennaRNA/mm.c
src/ViennaRNA/mm.h
src/ViennaRNA/model.c
src/ViennaRNA/model.h
src/ViennaRNA/move_set.c
src/ViennaRNA/move_set.h
src/ViennaRNA/multibranch_loops.h
src/ViennaRNA/naview.h
src/ViennaRNA/neighbor.h
src/ViennaRNA/pair_mat.h
src/ViennaRNA/params.h
src/ViennaRNA/part_func.h
src/ViennaRNA/part_func_co.h
src/ViennaRNA/part_func_up.h
src/ViennaRNA/part_func_window.h
src/ViennaRNA/perturbation_fold.c
src/ViennaRNA/perturbation_fold.h
src/ViennaRNA/pf_multifold.h
src/ViennaRNA/pk_plex.h
src/ViennaRNA/plex.c
src/ViennaRNA/plex.h
src/ViennaRNA/plex_functions.c
src/ViennaRNA/plot_aln.h
src/ViennaRNA/plot_layouts.h
src/ViennaRNA/plot_structure.h
src/ViennaRNA/plot_utils.h
src/ViennaRNA/profiledist.h
src/ViennaRNA/read_epars.h
src/ViennaRNA/ribo.h
src/ViennaRNA/sequence.h
src/ViennaRNA/snofold.c
src/ViennaRNA/snofold.h
src/ViennaRNA/snoop.c
src/ViennaRNA/snoop.h
src/ViennaRNA/stream_output.h
src/ViennaRNA/string_utils.h
src/ViennaRNA/stringdist.c
src/ViennaRNA/stringdist.h
src/ViennaRNA/structure_utils.h
src/ViennaRNA/structured_domains.h
src/ViennaRNA/subopt.h
src/ViennaRNA/subopt_zuker.h
src/ViennaRNA/svm_utils.h
src/ViennaRNA/treedist.c
src/ViennaRNA/treedist.h
src/ViennaRNA/units.h
src/ViennaRNA/unstructured_domains.c
src/ViennaRNA/unstructured_domains.h
src/ViennaRNA/utils.h
src/ViennaRNA/vrna_config.h
src/ViennaRNA/walk.h
src/ViennaRNA/wrap_dlib.cpp
src/ViennaRNA/wrap_dlib.h
src/ViennaRNA/backtrack/bt_exterior.c
src/ViennaRNA/backtrack/bt_exterior_f3.c
src/ViennaRNA/backtrack/bt_exterior_f5.c
src/ViennaRNA/backtrack/bt_gquad.c
src/ViennaRNA/backtrack/bt_hairpin.c
src/ViennaRNA/backtrack/bt_internal.c
src/ViennaRNA/backtrack/bt_multibranch.c
src/ViennaRNA/backtrack/exterior.h
src/ViennaRNA/backtrack/global.h
src/ViennaRNA/backtrack/gquad.h
src/ViennaRNA/backtrack/hairpin.h
src/ViennaRNA/backtrack/internal.h
src/ViennaRNA/backtrack/multibranch.h
src/ViennaRNA/combinatorics/basic.h
src/ViennaRNA/combinatorics/combinatorics.c
src/ViennaRNA/constraints/SHAPE.h
src/ViennaRNA/constraints/basic.h
src/ViennaRNA/constraints/constraints.c
src/ViennaRNA/constraints/exterior_sc.inc
src/ViennaRNA/constraints/exterior_sc_pf.inc
src/ViennaRNA/constraints/hairpin_sc.inc
src/ViennaRNA/constraints/hairpin_sc_pf.inc
src/ViennaRNA/constraints/hard.c
src/ViennaRNA/constraints/hard.h
src/ViennaRNA/constraints/hc_depot.inc
src/ViennaRNA/constraints/internal_sc.inc
src/ViennaRNA/constraints/internal_sc_pf.inc
src/ViennaRNA/constraints/ligand.c
src/ViennaRNA/constraints/ligand.h
src/ViennaRNA/constraints/multibranch_sc.inc
src/ViennaRNA/constraints/multibranch_sc_pf.inc
src/ViennaRNA/constraints/sc_cb_intern.h
src/ViennaRNA/constraints/sc_cb_mod.c
src/ViennaRNA/constraints/sc_cb_mod_parser.c
src/ViennaRNA/constraints/sc_cb_mod_wrappers.c
src/ViennaRNA/constraints/soft.c
src/ViennaRNA/constraints/soft.h
src/ViennaRNA/constraints/soft_cb_multi.c
src/ViennaRNA/constraints/soft_special.h
src/ViennaRNA/constraints/wrap_exterior_hc.inc
src/ViennaRNA/constraints/wrap_hairpin_hc.inc
src/ViennaRNA/constraints/wrap_internal_hc.inc
src/ViennaRNA/constraints/wrap_multibranch_hc.inc
src/ViennaRNA/data/transform.c
src/ViennaRNA/data/transform.h
src/ViennaRNA/datastructures/array.c
src/ViennaRNA/datastructures/array.h
src/ViennaRNA/datastructures/basic.h
src/ViennaRNA/datastructures/basic_datastructures.c
src/ViennaRNA/datastructures/char_stream.c
src/ViennaRNA/datastructures/char_stream.h
src/ViennaRNA/datastructures/dp_matrices.c
src/ViennaRNA/datastructures/dp_matrices.h
src/ViennaRNA/datastructures/hash_tables.c
src/ViennaRNA/datastructures/hash_tables.h
src/ViennaRNA/datastructures/heap.c
src/ViennaRNA/datastructures/heap.h
src/ViennaRNA/datastructures/lists.c
src/ViennaRNA/datastructures/lists.h
src/ViennaRNA/datastructures/sparse_mx.c
src/ViennaRNA/datastructures/sparse_mx.h
src/ViennaRNA/datastructures/stream_output.c
src/ViennaRNA/datastructures/stream_output.h
src/ViennaRNA/datastructures/string.c
src/ViennaRNA/datastructures/string.h
src/ViennaRNA/eval/basic.h
src/ViennaRNA/eval/eval_covariance.c
src/ViennaRNA/eval/eval_exterior.c
src/ViennaRNA/eval/eval_gquad.c
src/ViennaRNA/eval/eval_hairpin.c
src/ViennaRNA/eval/eval_internal.c
src/ViennaRNA/eval/eval_multibranch.c
src/ViennaRNA/eval/eval_structures.c
src/ViennaRNA/eval/eval_wrappers.c
src/ViennaRNA/eval/exp_eval_exterior.c
src/ViennaRNA/eval/exp_eval_hairpin.c
src/ViennaRNA/eval/exp_eval_internal.c
src/ViennaRNA/eval/exp_eval_multibranch.c
src/ViennaRNA/eval/exterior.h
src/ViennaRNA/eval/gquad.h
src/ViennaRNA/eval/hairpin.h
src/ViennaRNA/eval/internal.h
src/ViennaRNA/eval/multibranch.h
src/ViennaRNA/eval/structures.h
src/ViennaRNA/grammar/basic.h
src/ViennaRNA/grammar/gr_extension_mfe.c
src/ViennaRNA/grammar/gr_extension_pf.c
src/ViennaRNA/grammar/grammar.c
src/ViennaRNA/grammar/mfe.h
src/ViennaRNA/grammar/partfunc.h
src/ViennaRNA/intern/color_output.h
src/ViennaRNA/intern/gquad_helpers.h
src/ViennaRNA/intern/grammar_dat.h
src/ViennaRNA/intern/unistd_win.h
src/ViennaRNA/intern/zscore_dat.h
src/ViennaRNA/inverse/basic.h
src/ViennaRNA/inverse/inverse.c
src/ViennaRNA/io/commands.c
src/ViennaRNA/io/commands.h
src/ViennaRNA/io/file_formats.c
src/ViennaRNA/io/file_formats.h
src/ViennaRNA/io/file_formats_msa.c
src/ViennaRNA/io/file_formats_msa.h
src/ViennaRNA/io/io_utils.c
src/ViennaRNA/io/sanitize.c
src/ViennaRNA/io/sanitize.h
src/ViennaRNA/io/utils.h
src/ViennaRNA/landscape/findpath.c
src/ViennaRNA/landscape/findpath.h
src/ViennaRNA/landscape/local_neighbors.c
src/ViennaRNA/landscape/local_neighbors.inc
src/ViennaRNA/landscape/move.c
src/ViennaRNA/landscape/move.h
src/ViennaRNA/landscape/neighbor.c
src/ViennaRNA/landscape/neighbor.h
src/ViennaRNA/landscape/paths.h
src/ViennaRNA/landscape/walk.c
src/ViennaRNA/landscape/walk.h
src/ViennaRNA/loops/all.h
src/ViennaRNA/loops/external.h
src/ViennaRNA/loops/hairpin.h
src/ViennaRNA/loops/internal.h
src/ViennaRNA/loops/multibranch.h
src/ViennaRNA/math/fun_bin.c
src/ViennaRNA/math/fun_chain.c
src/ViennaRNA/math/fun_gaussian.c
src/ViennaRNA/math/fun_kde.c
src/ViennaRNA/math/fun_linear.c
src/ViennaRNA/math/fun_log.c
src/ViennaRNA/math/fun_logistic.c
src/ViennaRNA/math/functions.h
src/ViennaRNA/mfe/Lfold.c
src/ViennaRNA/mfe/alifold.c
src/ViennaRNA/mfe/cofold.c
src/ViennaRNA/mfe/exterior.h
src/ViennaRNA/mfe/fold.c
src/ViennaRNA/mfe/global.h
src/ViennaRNA/mfe/gquad.h
src/ViennaRNA/mfe/internal.h
src/ViennaRNA/mfe/local.h
src/ViennaRNA/mfe/mfe.c
src/ViennaRNA/mfe/mfe_exterior.c
src/ViennaRNA/mfe/mfe_exterior_window.c
src/ViennaRNA/mfe/mfe_gquad.c
src/ViennaRNA/mfe/mfe_internal.c
src/ViennaRNA/mfe/mfe_multibranch.c
src/ViennaRNA/mfe/mfe_window.c
src/ViennaRNA/mfe/mfe_window_wrappers.c
src/ViennaRNA/mfe/mfe_wrappers.c
src/ViennaRNA/mfe/multibranch.h
src/ViennaRNA/params/1.8.4_epars.h
src/ViennaRNA/params/1.8.4_intloops.h
src/ViennaRNA/params/basic.h
src/ViennaRNA/params/constants.h
src/ViennaRNA/params/convert.c
src/ViennaRNA/params/convert.h
src/ViennaRNA/params/default.c
src/ViennaRNA/params/default.h
src/ViennaRNA/params/intl11.h
src/ViennaRNA/params/intl11dH.h
src/ViennaRNA/params/intl21.h
src/ViennaRNA/params/intl21dH.h
src/ViennaRNA/params/intl22.h
src/ViennaRNA/params/intl22dH.h
src/ViennaRNA/params/io.c
src/ViennaRNA/params/io.h
src/ViennaRNA/params/params.c
src/ViennaRNA/params/ribosum.c
src/ViennaRNA/params/ribosum.h
src/ViennaRNA/params/salt.c
src/ViennaRNA/params/salt.h
src/ViennaRNA/params/special_const.c
src/ViennaRNA/params/special_const.h
src/ViennaRNA/params/svm_model_avg.inc
src/ViennaRNA/params/svm_model_sd.inc
src/ViennaRNA/partfunc/alipfold.c
src/ViennaRNA/partfunc/exterior.h
src/ViennaRNA/partfunc/global.h
src/ViennaRNA/partfunc/gquad.h
src/ViennaRNA/partfunc/internal.h
src/ViennaRNA/partfunc/local.h
src/ViennaRNA/partfunc/multibranch.h
src/ViennaRNA/partfunc/multifold.h
src/ViennaRNA/partfunc/part_func_co.c
src/ViennaRNA/partfunc/part_func_up.c
src/ViennaRNA/partfunc/partfunc.c
src/ViennaRNA/partfunc/pf_exterior.c
src/ViennaRNA/partfunc/pf_fold.c
src/ViennaRNA/partfunc/pf_gquad.c
src/ViennaRNA/partfunc/pf_internal.c
src/ViennaRNA/partfunc/pf_multibranch.c
src/ViennaRNA/partfunc/pf_multifold.c
src/ViennaRNA/partfunc/pf_window.c
src/ViennaRNA/partfunc/pf_wrappers.c
src/ViennaRNA/plotting/alignments.c
src/ViennaRNA/plotting/alignments.h
src/ViennaRNA/plotting/eps.c
src/ViennaRNA/plotting/gml.c
src/ViennaRNA/plotting/layouts.c
src/ViennaRNA/plotting/layouts.h
src/ViennaRNA/plotting/plot_utils.c
src/ViennaRNA/plotting/probabilities.c
src/ViennaRNA/plotting/probabilities.h
src/ViennaRNA/plotting/ps_helpers.inc
src/ViennaRNA/plotting/ssv.c
src/ViennaRNA/plotting/structures.c
src/ViennaRNA/plotting/structures.h
src/ViennaRNA/plotting/svg.c
src/ViennaRNA/plotting/utils.h
src/ViennaRNA/plotting/xrna.c
src/ViennaRNA/plotting/RNApuzzler/RNApuzzler.c
src/ViennaRNA/plotting/RNApuzzler/RNApuzzler.h
src/ViennaRNA/plotting/RNApuzzler/RNAturtle.c
src/ViennaRNA/plotting/RNApuzzler/RNAturtle.h
src/ViennaRNA/plotting/RNApuzzler/headers/AABB_struct.h
src/ViennaRNA/plotting/RNApuzzler/headers/boundingBoxes_struct.h
src/ViennaRNA/plotting/RNApuzzler/headers/configArc_struct.h
src/ViennaRNA/plotting/RNApuzzler/headers/config_struct.h
src/ViennaRNA/plotting/RNApuzzler/headers/configtree_struct.h
src/ViennaRNA/plotting/RNApuzzler/headers/tBaseInformation_struct.h
src/ViennaRNA/plotting/RNApuzzler/includes/boundingBoxes.inc
src/ViennaRNA/plotting/RNApuzzler/includes/boundingWedge.inc
src/ViennaRNA/plotting/RNApuzzler/includes/calcDeltas.inc
src/ViennaRNA/plotting/RNApuzzler/includes/configtree.inc
src/ViennaRNA/plotting/RNApuzzler/includes/coordinates.inc
src/ViennaRNA/plotting/RNApuzzler/includes/definitions.inc
src/ViennaRNA/plotting/RNApuzzler/includes/drawingconfig.inc
src/ViennaRNA/plotting/RNApuzzler/includes/handleAncestorIntersections.inc
src/ViennaRNA/plotting/RNApuzzler/includes/handleConfigChanges.inc
src/ViennaRNA/plotting/RNApuzzler/includes/handleSiblingIntersections.inc
src/ViennaRNA/plotting/RNApuzzler/includes/intersectLevelBoundingBoxes.inc
src/ViennaRNA/plotting/RNApuzzler/includes/intersectLevelLines.inc
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src/ViennaRNA/plotting/RNApuzzler/includes/intersectionType.inc
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src/ViennaRNA/plotting/RNApuzzler/includes/postscriptArcs.inc
src/ViennaRNA/plotting/RNApuzzler/includes/resolveExteriorChildIntersections.inc
src/ViennaRNA/plotting/RNApuzzler/includes/resolveIntersections.inc
src/ViennaRNA/plotting/RNApuzzler/includes/rotationAngle.inc
src/ViennaRNA/plotting/RNApuzzler/includes/svgArcs.inc
src/ViennaRNA/plotting/RNApuzzler/includes/vector_math.inc
src/ViennaRNA/plotting/naview/naview.c
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src/ViennaRNA/probabilities/basepairs.h
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src/ViennaRNA/probing/strategy_nlogp.c
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src/ViennaRNA/search/BoyerMoore.c
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src/ViennaRNA/sequences/msa.c
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src/ViennaRNA/subopt/zuker.h
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src/ViennaRNA/utils/basic.h
src/ViennaRNA/utils/cpu.c
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src/ViennaRNA/utils/higher_order_functions_avx512.c
src/ViennaRNA/utils/higher_order_functions_sse41.c
src/ViennaRNA/utils/log.c
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src/ViennaRNA/utils/structures.h
src/ViennaRNA/utils/svm.h
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src/ViennaRNA/utils/units.c
src/ViennaRNA/utils/units.h
src/ViennaRNA/utils/utils.c
src/ViennaRNA/zscore/basic.h
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