bin/eternafold
bin/eternafold-bin/MakeDefaults.pl
bin/eternafold-bin/api_test
bin/eternafold-bin/contrafold
bin/eternafold-bin/roc_area.pl
bin/eternafold-bin/score_directory.pl
bin/eternafold-bin/score_prediction
etc/conda/activate.d/eternafold_activate.sh
etc/conda/deactivate.d/eternafold_deactivate.sh
lib/eternafold-lib/LICENSE
lib/eternafold-lib/LinearFold-E.patch
lib/eternafold-lib/LinearPartition-E.patch
lib/eternafold-lib/README.md
lib/eternafold-lib/README_LinearFold-E_patch.md
lib/eternafold-lib/build_env_setup.sh
lib/eternafold-lib/conda_build.sh
lib/eternafold-lib/datalists/README.md
lib/eternafold-lib/datalists/generate_datalist.sh
lib/eternafold-lib/datalists/write_all_datalists.sh
lib/eternafold-lib/datasets_in_fasta_form/EternaBench_datasets/EB_ChemMapping_Filtered.fasta
lib/eternafold-lib/datasets_in_fasta_form/EternaBench_datasets/EB_ChemMapping_unfiltered.fasta
lib/eternafold-lib/datasets_in_fasta_form/EternaBench_datasets/EB_Riboswitch_Filtered.fasta
lib/eternafold-lib/datasets_in_fasta_form/EternaBench_datasets/EB_Riboswitch_unfiltered.fasta
lib/eternafold-lib/datasets_in_fasta_form/README.md
lib/eternafold-lib/datasets_in_fasta_form/holdout_datasets/ChemMappingData_holdout.fasta
lib/eternafold-lib/datasets_in_fasta_form/holdout_datasets/RiboswitchData_holdout.fasta
lib/eternafold-lib/datasets_in_fasta_form/holdout_datasets/S-Processed-VAL.fasta
lib/eternafold-lib/datasets_in_fasta_form/test_datasets/ExternalData.fasta
lib/eternafold-lib/datasets_in_fasta_form/test_datasets/ExternalData_window1200_uniq.fasta
lib/eternafold-lib/datasets_in_fasta_form/test_datasets/ExternalData_window300_uniq.fasta
lib/eternafold-lib/datasets_in_fasta_form/test_datasets/ExternalData_window600_uniq.fasta
lib/eternafold-lib/datasets_in_fasta_form/test_datasets/ExternalData_window900_uniq.fasta
lib/eternafold-lib/datasets_in_fasta_form/test_datasets/S-Processed-TES.fasta
lib/eternafold-lib/datasets_in_fasta_form/test_datasets/archiveII_filt_80_NR.fasta
lib/eternafold-lib/datasets_in_fasta_form/test_datasets/archiveII_original.fasta
lib/eternafold-lib/datasets_in_fasta_form/train_datasets/All_EternaFold_training_data.fasta
lib/eternafold-lib/datasets_in_fasta_form/train_datasets/ChemMappingData_train.fasta
lib/eternafold-lib/datasets_in_fasta_form/train_datasets/RiboswitchData_train.fasta
lib/eternafold-lib/datasets_in_fasta_form/train_datasets/S-Processed-TRA.fasta
lib/eternafold-lib/input_data.zip
lib/eternafold-lib/metadata_conda_debug.yaml
lib/eternafold-lib/parameters/EternaFoldParams.v1
lib/eternafold-lib/parameters/EternaFoldParams_PLUS_POTENTIALS.v1
lib/eternafold-lib/parameters/LICENSE
lib/eternafold-lib/parameters/README.md
lib/eternafold-lib/scripts/ConvertRFAM
lib/eternafold-lib/scripts/ConvertRFAM.cc
lib/eternafold-lib/scripts/README.md
lib/eternafold-lib/scripts/score_riboswitch_foldchange.sh
lib/eternafold-lib/scripts/score_single_structure_prediction.sh
lib/eternafold-lib/src/.nfs0000000272a7723b000013b6
lib/eternafold-lib/src/BundleMethod.hpp
lib/eternafold-lib/src/BundleMethod.ipp
lib/eternafold-lib/src/CGLinear.hpp
lib/eternafold-lib/src/CGLinear.ipp
lib/eternafold-lib/src/CGOptimizationWrapper.hpp
lib/eternafold-lib/src/CGOptimizationWrapper.ipp
lib/eternafold-lib/src/ComputationEngine.hpp
lib/eternafold-lib/src/ComputationEngine.ipp
lib/eternafold-lib/src/ComputationWrapper.hpp
lib/eternafold-lib/src/ComputationWrapper.ipp
lib/eternafold-lib/src/Config.hpp
lib/eternafold-lib/src/Contrafold.cpp
lib/eternafold-lib/src/Contrafold.o
lib/eternafold-lib/src/Defaults.ipp
lib/eternafold-lib/src/DistributedComputation.hpp
lib/eternafold-lib/src/DistributedComputation.ipp
lib/eternafold-lib/src/EM.hpp
lib/eternafold-lib/src/EM.ipp
lib/eternafold-lib/src/EncapsulatedPostScript.cpp
lib/eternafold-lib/src/EncapsulatedPostScript.hpp
lib/eternafold-lib/src/FileDescription.cpp
lib/eternafold-lib/src/FileDescription.hpp
lib/eternafold-lib/src/FileDescription.o
lib/eternafold-lib/src/GammaMLE.hpp
lib/eternafold-lib/src/GammaMLE.ipp
lib/eternafold-lib/src/InferenceEngine.hpp
lib/eternafold-lib/src/InferenceEngine.ipp
lib/eternafold-lib/src/InnerOptimizationWrapper.hpp
lib/eternafold-lib/src/InnerOptimizationWrapper.ipp
lib/eternafold-lib/src/InnerOptimizationWrapperBundleMethod.hpp
lib/eternafold-lib/src/InnerOptimizationWrapperBundleMethod.ipp
lib/eternafold-lib/src/InnerOptimizationWrapperEM.hpp
lib/eternafold-lib/src/InnerOptimizationWrapperEM.ipp
lib/eternafold-lib/src/InnerOptimizationWrapperLBFGS.hpp
lib/eternafold-lib/src/InnerOptimizationWrapperLBFGS.ipp
lib/eternafold-lib/src/InnerOptimizationWrapperStochasticGradient.hpp
lib/eternafold-lib/src/InnerOptimizationWrapperStochasticGradient.ipp
lib/eternafold-lib/src/InnerOptimizationWrapperSubgradientMethod.hpp
lib/eternafold-lib/src/InnerOptimizationWrapperSubgradientMethod.ipp
lib/eternafold-lib/src/InnerOptimizationWrapperViterbi.hpp
lib/eternafold-lib/src/InnerOptimizationWrapperViterbi.ipp
lib/eternafold-lib/src/LBFGS.hpp
lib/eternafold-lib/src/LBFGS.ipp
lib/eternafold-lib/src/LineSearch.hpp
lib/eternafold-lib/src/LineSearch.ipp
lib/eternafold-lib/src/LogSpace.hpp
lib/eternafold-lib/src/MakeCoords.cpp
lib/eternafold-lib/src/MakeCoords.hpp
lib/eternafold-lib/src/MakeDefaults.pl
lib/eternafold-lib/src/Makefile
lib/eternafold-lib/src/OptimizationWrapper.hpp
lib/eternafold-lib/src/OptimizationWrapper.ipp
lib/eternafold-lib/src/Options.cpp
lib/eternafold-lib/src/Options.hpp
lib/eternafold-lib/src/Options.o
lib/eternafold-lib/src/OuterOptimizationWrapper.hpp
lib/eternafold-lib/src/OuterOptimizationWrapper.ipp
lib/eternafold-lib/src/ParameterManager.hpp
lib/eternafold-lib/src/ParameterManager.ipp
lib/eternafold-lib/src/PlotRNA.cpp
lib/eternafold-lib/src/README.md
lib/eternafold-lib/src/SStruct.cpp
lib/eternafold-lib/src/SStruct.hpp
lib/eternafold-lib/src/SStruct.o
lib/eternafold-lib/src/ScorePrediction.cpp
lib/eternafold-lib/src/ScorePrediction.o
lib/eternafold-lib/src/SparseMatrix.hpp
lib/eternafold-lib/src/SparseMatrix.ipp
lib/eternafold-lib/src/SubgradientMethod.hpp
lib/eternafold-lib/src/SubgradientMethod.ipp
lib/eternafold-lib/src/Utilities.cpp
lib/eternafold-lib/src/Utilities.hpp
lib/eternafold-lib/src/Utilities.ipp
lib/eternafold-lib/src/Utilities.o
lib/eternafold-lib/src/api_test
lib/eternafold-lib/src/api_test.cpp
lib/eternafold-lib/src/api_test.o
lib/eternafold-lib/src/batch_score_prediction.sh
lib/eternafold-lib/src/contrafold
lib/eternafold-lib/src/contrafold.params.complementary
lib/eternafold-lib/src/contrafold.params.noncomplementary
lib/eternafold-lib/src/contrafold.params.profile
lib/eternafold-lib/src/contrafold_api.cpp
lib/eternafold-lib/src/contrafold_api.hpp
lib/eternafold-lib/src/contrafold_api.o
lib/eternafold-lib/src/rand.h
lib/eternafold-lib/src/roc_area.pl
lib/eternafold-lib/src/score_directory.pl
lib/eternafold-lib/src/score_prediction
lib/eternafold-lib/src/tmp.seq
lib/eternafold-lib/test.seq
