MANIFEST.in
README
setup.py
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/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853305438/work/hyphy-python-0.1.6/hyphy-src/src/new/bgm.cpp
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/private/tmp/workspace/miniconda/conda-bld/python-hyphy-python_1517853305438/work/hyphy-python-0.1.6/hyphy-src/src/utils/hyphyunixutils.cpp
HyPhy/__init__.py
Link/THyPhy.cpp
Link/THyPhy.h
SWIGWrappers/THyPhy_py3.cpp
SWIGWrappers/THyPhy_python.cpp
hyphy-src/.gitignore
hyphy-src/CMakeLists.txt
hyphy-src/LICENSE
hyphy-src/README.md
hyphy-src/package.json
hyphy-src/CMakeWin32/CMakeLists.txt
hyphy-src/Examples/BatchLanguage/MatrixIndexing.bf
hyphy-src/Examples/BatchLanguage/profile_test.bf
hyphy-src/Examples/Categories/definitions+MLE.bf
hyphy-src/Examples/Categories/definitions.bf
hyphy-src/Examples/Categories/definitions2.bf
hyphy-src/Examples/Categories/definitions3.bf
hyphy-src/Examples/Categories/displayFunction.bf
hyphy-src/Examples/Categories/data/aspectrin.nuc
hyphy-src/Examples/ConstraintDefinition/ReplicateConstraint1.bf
hyphy-src/Examples/ConstraintDefinition/ReplicateConstraint2.bf
hyphy-src/Examples/ConstraintDefinition/ReplicateConstraint3.bf
hyphy-src/Examples/ConstraintDefinition/shared.bf
hyphy-src/Examples/ConstraintDefinition/data/hiv.seq
hyphy-src/Examples/DataFilters/HKY852blocks.bf
hyphy-src/Examples/DataFilters/HKY852blocks2models.bf
hyphy-src/Examples/DataFilters/data/actin2.flt
hyphy-src/Examples/MoreComplexModels/ExonIntron.bf
hyphy-src/Examples/MoreComplexModels/aa.bf
hyphy-src/Examples/MoreComplexModels/Models/EI.mdl
hyphy-src/Examples/MoreComplexModels/Models/MG94x2.mdl
hyphy-src/Examples/MoreComplexModels/data/3.seq
hyphy-src/Examples/MoreComplexModels/data/stewart.aa
hyphy-src/Examples/MoreComplexModels/data/ubiq.flt
hyphy-src/Examples/SimpleAnalyses/F81.bf
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hyphy-src/Examples/SimpleAnalyses/JC69.bf
hyphy-src/Examples/SimpleAnalyses/K2P.bf
hyphy-src/Examples/SimpleAnalyses/K2Pshared.bf
hyphy-src/Examples/SimpleAnalyses/Non-Rev.bf
hyphy-src/Examples/SimpleAnalyses/REV.bf
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hyphy-src/Examples/SimpleAnalyses/data/hiv.nuc
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hyphy-src/Examples/SimpleConstraints/F81relratio.bf
hyphy-src/Examples/SimpleConstraints/HKY85relrate.bf
hyphy-src/Examples/SimpleConstraints/HKY85relratio.bf
hyphy-src/Examples/SimpleConstraints/MolecularClockF81.bf
hyphy-src/Examples/SimpleConstraints/MolecularClockHKY85.bf
hyphy-src/Examples/SimpleConstraints/data/3.seq
hyphy-src/Examples/SimpleConstraints/data/aspectrin1.nuc
hyphy-src/Examples/SimpleConstraints/data/aspectrin2.nuc
hyphy-src/Examples/SimpleConstraints/data/molclock.seq
hyphy-src/Examples/Simulation/PBootstrapHetRates.bf
hyphy-src/Examples/Simulation/ParametricBootstrap.bf
hyphy-src/Examples/Simulation/RelativeRatePBS.bf
hyphy-src/Examples/Simulation/data/3.seq
hyphy-src/Examples/Simulation/data/hiv.nuc
hyphy-src/cmake/FindOpenCL.cmake
hyphy-src/cmake/cmake_uninstall.cmake.in
hyphy-src/contrib/cl2hdr.c
hyphy-src/contrib/SQLite-3.8.2/shell.c
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hyphy-src/contrib/SQLite-3.8.2/sqlite3ext.h
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hyphy-src/contrib/gtest-1.7.0/samples/sample1.h
hyphy-src/contrib/gtest-1.7.0/samples/sample10_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample1_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample2.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest-linked_ptr_test.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest-options_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-param-test2_test.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest-tuple_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-typed-test2_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-typed-test_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-typed-test_test.h
hyphy-src/contrib/gtest-1.7.0/test/gtest-unittest-api_test.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest_break_on_failure_unittest.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_break_on_failure_unittest_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_catch_exceptions_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_catch_exceptions_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_color_test.py
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hyphy-src/contrib/gtest-1.7.0/test/gtest_env_var_test.py
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hyphy-src/contrib/gtest-1.7.0/test/gtest_environment_test.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest_filter_unittest_.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest_list_tests_unittest_.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest_no_test_unittest.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest_output_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_output_test_golden_lin.txt
hyphy-src/contrib/gtest-1.7.0/test/gtest_pred_impl_unittest.cc
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hyphy-src/res/TemplateBatchFiles/Distances/TN93
hyphy-src/res/TemplateBatchFiles/Distances/TN93_RV
hyphy-src/res/TemplateBatchFiles/Distances/Unaligned_LZ
hyphy-src/res/TemplateBatchFiles/Distances/Unaligned_LZ_FR
hyphy-src/res/TemplateBatchFiles/Distances/p_Distance
hyphy-src/res/TemplateBatchFiles/Distances/p_Distance_aa
hyphy-src/res/TemplateBatchFiles/Distances/p_Distance_binary
hyphy-src/res/TemplateBatchFiles/Distances/p_Distance_codon
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hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_2.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_3.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_4.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_PHASE_5.bf
hyphy-src/res/TemplateBatchFiles/FUBAR_HBL/FUBAR_tools.ibf
hyphy-src/res/TemplateBatchFiles/GUI/crayolaColors.def
hyphy-src/res/TemplateBatchFiles/Samplers/lhc.bf
hyphy-src/res/TemplateBatchFiles/Samplers/lhc_supp.ibf
hyphy-src/res/TemplateBatchFiles/Samplers/sir.bf
hyphy-src/res/TemplateBatchFiles/Samplers/srs.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/190
hyphy-src/res/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/CF3x4.bf
hyphy-src/res/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Default
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM+F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/ECM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/EIAA.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/EX.dat
hyphy-src/res/TemplateBatchFiles/TemplateModels/EX.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/F81.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/F81_binary.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/F84.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/F84P.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/GRM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/GY94.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/GY94.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/GY94w9.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HKY85.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/JC69.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Jones.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Jones_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/K2P.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/K3ST.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/LCAP.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MEC.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94custom.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MG94x2.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/MGwAA.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/MGwEX.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/NRM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/PCH
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNA16.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNA16A
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAEqualInput
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAF81
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAREV
hyphy-src/res/TemplateBatchFiles/TemplateModels/RNAREV_1
hyphy-src/res/TemplateBatchFiles/TemplateModels/S4
hyphy-src/res/TemplateBatchFiles/TemplateModels/STGRM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/TrN.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/UniversalCode.def
hyphy-src/res/TemplateBatchFiles/TemplateModels/WAG.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/WAG_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
hyphy-src/res/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
hyphy-src/res/TemplateBatchFiles/TemplateModels/custm4x4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/defineGamma.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/defineHM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/fitness.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/models.lst
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtMAM.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtREV.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/reducedREV.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/rtREV.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/rtREV_F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
hyphy-src/res/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
hyphy-src/res/TemplateBatchFiles/Utility/AncestralMapper.bf
hyphy-src/res/TemplateBatchFiles/Utility/BranchLengthFitters.bf
hyphy-src/res/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
hyphy-src/res/TemplateBatchFiles/Utility/CodonTools.bf
hyphy-src/res/TemplateBatchFiles/Utility/DBTools.ibf
hyphy-src/res/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
hyphy-src/res/TemplateBatchFiles/Utility/GrabBag.bf
hyphy-src/res/TemplateBatchFiles/Utility/HXB2Mapper.bf
hyphy-src/res/TemplateBatchFiles/Utility/LocalMGREV.bf
hyphy-src/res/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf
hyphy-src/res/TemplateBatchFiles/Utility/MPITools.bf
hyphy-src/res/TemplateBatchFiles/Utility/NJ.bf
hyphy-src/res/TemplateBatchFiles/Utility/PS_Plotters.bf
hyphy-src/res/TemplateBatchFiles/Utility/PostScript.bf
hyphy-src/res/TemplateBatchFiles/Utility/ProbabilityDistributions.bf
hyphy-src/res/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf
hyphy-src/res/TemplateBatchFiles/Utility/TreeFunctions.bf
hyphy-src/res/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf
hyphy-src/res/TemplateBatchFiles/lib2014/IOFunctions.bf
hyphy-src/res/TemplateBatchFiles/lib2014/UtilityFunctions.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/DNA.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/codon.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/frequencies.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/model_functions.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/parameters.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/rate_variation.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/terms.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/DNA/GTR.bf
hyphy-src/res/TemplateBatchFiles/lib2014/models/codon/MG_REV.bf
hyphy-src/res/TemplateBatchFiles/lib2014/tasks/estimators.bf
hyphy-src/res/TopologyInference/Exhaustive_Search
hyphy-src/res/TopologyInference/Neighbor_Joining
hyphy-src/res/TopologyInference/Sequential_Addition
hyphy-src/res/TopologyInference/Star_Decomposition
hyphy-src/res/TopologyInference/Support/branchSwappingFunctions.bf
hyphy-src/res/TopologyInference/Support/doNNISwap.bf
hyphy-src/res/TopologyInference/Support/doSPRSwap.bf
hyphy-src/res/TreeAddIns/Splits
hyphy-src/res/TreeAddIns/Tree Statistics
hyphy-src/res/UserAddins/AAContent
hyphy-src/res/UserAddins/BatchFileByURL
hyphy-src/res/UserAddins/BranchLengthCI
hyphy-src/res/UserAddins/CodonMutationToTreeMapper
hyphy-src/res/UserAddins/CountSubstitutions
hyphy-src/res/UserAddins/ExportLikelihoodFunction
hyphy-src/res/UserAddins/GenBankSequences
hyphy-src/res/UserAddins/LRT
hyphy-src/res/UserAddins/ListUserFunctions
hyphy-src/res/UserAddins/MapSubstitutions
hyphy-src/res/UserAddins/MeanPairwiseDivergence
hyphy-src/res/UserAddins/MeanPairwiseDivergenceSubset
hyphy-src/res/UserAddins/ModelCounter
hyphy-src/res/UserAddins/RecombinationProcessor.bf
hyphy-src/res/UserAddins/SimulateFromLF
hyphy-src/res/UserAddins/Tidbits
hyphy-src/res/UserAddins/Includes/ChooseALF.ibf
hyphy-src/res/UserAddins/Includes/MappersHelp.ibf
hyphy-src/res/UserAddins/Includes/MappersHelpAA.ibf
hyphy-src/res/UserAddins/OldAddins/AAMutationCounter
hyphy-src/res/UserAddins/OldAddins/CodonMutationToTreeMapper.bf
hyphy-src/res/UserAddins/OldAddins/ColorPSTree
hyphy-src/res/UserAddins/OldAddins/ConvergentAndParallel
hyphy-src/res/UserAddins/OldAddins/CopyBranchLengths
hyphy-src/res/UserAddins/OldAddins/DashPSTree
hyphy-src/res/UserAddins/OldAddins/ExpsPerDirection
hyphy-src/res/UserAddins/OldAddins/FilterAssignments
hyphy-src/res/UserAddins/OldAddins/InferredAASubstitutionsCounter
hyphy-src/res/UserAddins/OldAddins/LocaldNdS
hyphy-src/res/UserAddins/OldAddins/ModelFitSummary
hyphy-src/res/UserAddins/OldAddins/ModelFitSummaryAA
hyphy-src/res/UserAddins/OldAddins/Multiclass DN DS inference
hyphy-src/res/UserAddins/OldAddins/PartitionBranchesByClasses
hyphy-src/res/UserAddins/OldAddins/PredictivePosteriorP
hyphy-src/res/UserAddins/OldAddins/RNARateMatrix
hyphy-src/res/UserAddins/OldAddins/SimulateAndTabDN_DS
hyphy-src/res/UserAddins/OldAddins/SimulateFromLF
hyphy-src/res/UserAddins/OldAddins/TreeLengthConstraint
hyphy-src/res/UserAddins/OldAddins/dNanddSTrees.bf
hyphy-src/res/UserAddins/OldAddins/dS and dN factors
hyphy-src/res/data/brown.nuc
hyphy-src/res/data/integrase_BDA.nex
hyphy-src/res/data/p51.aa
hyphy-src/res/data/p51.nex
hyphy-src/scripts/build.sh
hyphy-src/scripts/buildFromSVN.sh
hyphy-src/scripts/buildMinGWFromSVN.sh
hyphy-src/scripts/build_mingw.sh
hyphy-src/scripts/build_mingw_MEGA.sh
hyphy-src/scripts/build_mingw_gui.sh
hyphy-src/scripts/gtk_build.sh
hyphy-src/scripts/intelCCbuild.sh
hyphy-src/src/core/_hyExecutionContext.cpp
hyphy-src/src/core/alignment.cpp
hyphy-src/src/core/avllist.cpp
hyphy-src/src/core/avllistx.cpp
hyphy-src/src/core/avllistxl.cpp
hyphy-src/src/core/baseobj.cpp
hyphy-src/src/core/batchlan.cpp
hyphy-src/src/core/batchlan2.cpp
hyphy-src/src/core/batchlanhelpers.cpp
hyphy-src/src/core/batchlanruntime.cpp
hyphy-src/src/core/calcnode.cpp
hyphy-src/src/core/calcnode2.cpp
hyphy-src/src/core/category.cpp
hyphy-src/src/core/classes.cp
hyphy-src/src/core/constant.cpp
hyphy-src/src/core/error.cpp
hyphy-src/src/core/fisher_exact.cpp
hyphy-src/src/core/formula.cpp
hyphy-src/src/core/fstring.cpp
hyphy-src/src/core/likefunc.cpp
hyphy-src/src/core/likefunc2.cpp
hyphy-src/src/core/likefuncocl.cpp
hyphy-src/src/core/list.cpp
hyphy-src/src/core/mathobj.cpp
hyphy-src/src/core/matrix.cpp
hyphy-src/src/core/nexus.cpp
hyphy-src/src/core/operation.cpp
hyphy-src/src/core/parser.cpp
hyphy-src/src/core/parser2.cpp
hyphy-src/src/core/polynoml.cpp
hyphy-src/src/core/ptr_array.cp
hyphy-src/src/core/regex.cpp
hyphy-src/src/core/sequence.cpp
hyphy-src/src/core/simplelist.cpp
hyphy-src/src/core/site.cpp
hyphy-src/src/core/stack.cpp
hyphy-src/src/core/strings.cpp
hyphy-src/src/core/trie.cpp
hyphy-src/src/core/variable.cpp
hyphy-src/src/core/variablecontainer.cpp
hyphy-src/src/core/include/_hyExecutionContext.h
hyphy-src/src/core/include/alignment.h
hyphy-src/src/core/include/avllist.h
hyphy-src/src/core/include/avllistx.h
hyphy-src/src/core/include/avllistxl.h
hyphy-src/src/core/include/baseobj.h
hyphy-src/src/core/include/batchlan.h
hyphy-src/src/core/include/calcnode.h
hyphy-src/src/core/include/category.h
hyphy-src/src/core/include/classes.h
hyphy-src/src/core/include/constant.h
hyphy-src/src/core/include/defines.h
hyphy-src/src/core/include/errorfns.h
hyphy-src/src/core/include/formula.h
hyphy-src/src/core/include/fstring.h
hyphy-src/src/core/include/gnuregex.h
hyphy-src/src/core/include/hy_strings.h
hyphy-src/src/core/include/likefunc.h
hyphy-src/src/core/include/list.h
hyphy-src/src/core/include/mathobj.h
hyphy-src/src/core/include/matrix.h
hyphy-src/src/core/include/mypthread.h
hyphy-src/src/core/include/operation.h
hyphy-src/src/core/include/parser.h
hyphy-src/src/core/include/polynoml.h
hyphy-src/src/core/include/sequence.h
hyphy-src/src/core/include/simplelist.h
hyphy-src/src/core/include/site.h
hyphy-src/src/core/include/stack.h
hyphy-src/src/core/include/trie.h
hyphy-src/src/core/include/variable.h
hyphy-src/src/core/include/variablecontainer.h
hyphy-src/src/gui/HYBaseGUI.cpp
hyphy-src/src/gui/HYChartWindow.cpp
hyphy-src/src/gui/HYComponent.cpp
hyphy-src/src/gui/HYConsoleWindow.cpp
hyphy-src/src/gui/HYDBWindow.cpp
hyphy-src/src/gui/HYDataPanel.cpp
hyphy-src/src/gui/HYDialogDefs.cpp
hyphy-src/src/gui/HYEventTypes.cpp
hyphy-src/src/gui/HYGraphicPane.cpp
hyphy-src/src/gui/HYModelWindow.cpp
hyphy-src/src/gui/HYObjectInspector.cpp
hyphy-src/src/gui/HYParameterTable.cpp
hyphy-src/src/gui/HYSharedMain.cpp
hyphy-src/src/gui/HYTreePanel.cpp
hyphy-src/src/gui/HYWindow.cpp
hyphy-src/src/gui/preferences.cpp
hyphy-src/src/gui/Components/HYButton.cpp
hyphy-src/src/gui/Components/HYButtonBar.cpp
hyphy-src/src/gui/Components/HYCheckBox.cpp
hyphy-src/src/gui/Components/HYLabel.cpp
hyphy-src/src/gui/Components/HYPullDown.cpp
hyphy-src/src/gui/Components/HYSequencePanel.cpp
hyphy-src/src/gui/Components/HYTable.cpp
hyphy-src/src/gui/Components/HYTextBox.cpp
hyphy-src/src/gui/gtk/HYPlatformComponent.cpp
hyphy-src/src/gui/gtk/HYPlatformGraphicPane.cpp
hyphy-src/src/gui/gtk/HYPlatformUtils.cpp
hyphy-src/src/gui/gtk/HYPlatformWindow.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformButton.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformButtonBar.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformCheckBox.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformLabel.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformPullDown.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformSequencePane.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformTable.cpp
hyphy-src/src/gui/gtk/Components/HYPlatformTextBox.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformBootsrapWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformChartWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformConsoleWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformDBWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformDataPanel.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformGWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformModelWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformPWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformParameterTable.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformTWindow.cpp
hyphy-src/src/gui/gtk/WindowClasses/HYPlatformTreePanel.cpp
hyphy-src/src/gui/gtk/include/HYPlatformComponent.h
hyphy-src/src/gui/gtk/include/HYPlatformGraphicPane.h
hyphy-src/src/gui/gtk/include/HYPlatformWindow.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformButton.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformButtonBar.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformCheckbox.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformLabel.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformPullDown.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformTable.h
hyphy-src/src/gui/gtk/include/Components/HYPlatformTextbox.h
hyphy-src/src/gui/include/HYBaseGUI.h
hyphy-src/src/gui/include/HYDialogs.h
hyphy-src/src/gui/include/HYEventTypes.h
hyphy-src/src/gui/include/HYGraphicPane.h
hyphy-src/src/gui/include/HYObjectInspector.h
hyphy-src/src/gui/include/HYSharedMain.h
hyphy-src/src/gui/include/HYTableWindow.h
hyphy-src/src/gui/include/HYUtils.h
hyphy-src/src/gui/include/HYWindow.h
hyphy-src/src/gui/include/preferences.h
hyphy-src/src/gui/include/shared_main.h
hyphy-src/src/gui/include/Components/HYButton.h
hyphy-src/src/gui/include/Components/HYButtonBar.h
hyphy-src/src/gui/include/Components/HYCanvas.h
hyphy-src/src/gui/include/Components/HYComponent.h
hyphy-src/src/gui/include/Components/HYLabel.h
hyphy-src/src/gui/include/Components/HYList.h
hyphy-src/src/gui/include/Components/HYPullDown.h
hyphy-src/src/gui/include/Components/HYSequencePanel.h
hyphy-src/src/gui/include/Components/HYTableComponent.h
hyphy-src/src/gui/include/Components/HYTextBox.h
hyphy-src/src/gui/include/WindowClasses/HYChartWindow.h
hyphy-src/src/gui/include/WindowClasses/HYConsoleWindow.h
hyphy-src/src/gui/include/WindowClasses/HYDBWindow.h
hyphy-src/src/gui/include/WindowClasses/HYDataPanel.h
hyphy-src/src/gui/include/WindowClasses/HYGWindow.h
hyphy-src/src/gui/include/WindowClasses/HYModelWindow.h
hyphy-src/src/gui/include/WindowClasses/HYParameterTable.h
hyphy-src/src/gui/include/WindowClasses/HYTreePanel.h
hyphy-src/src/gui/mac/Docs.icns
hyphy-src/src/gui/mac/HYPHY.icns
hyphy-src/src/gui/mac/HYPHYMP.icns
hyphy-src/src/gui/mac/HYPlatformComponent.cpp
hyphy-src/src/gui/mac/HYPlatformGraphicPane.cpp
hyphy-src/src/gui/mac/HYPlatformUtils.cpp
hyphy-src/src/gui/mac/HYPlatformWindow.cpp
hyphy-src/src/gui/mac/HyPhy.rsrc
hyphy-src/src/gui/mac/Info.plist
hyphy-src/src/gui/mac/hydialogs.cpp
hyphy-src/src/gui/mac/iHyPhyDebug.rsrc
hyphy-src/src/gui/mac/plist.r
hyphy-src/src/gui/mac/plist.xml
hyphy-src/src/gui/mac/plistmp.r
hyphy-src/src/gui/mac/Components/HYPlatformButton.cpp
hyphy-src/src/gui/mac/Components/HYPlatformButtonBar.cpp
hyphy-src/src/gui/mac/Components/HYPlatformCheckBox.cpp
hyphy-src/src/gui/mac/Components/HYPlatformLabel.cpp
hyphy-src/src/gui/mac/Components/HYPlatformList.cpp
hyphy-src/src/gui/mac/Components/HYPlatformPullDown.cpp
hyphy-src/src/gui/mac/Components/HYPlatformSequencePane.cpp
hyphy-src/src/gui/mac/Components/HYPlatformTable.cpp
hyphy-src/src/gui/mac/Components/HYPlatformTextBox.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformBootsrapWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformChartWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformConsoleWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformDBWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformDataPanel.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformGWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformModelWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformPWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformParameterTable.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformTWindow.cpp
hyphy-src/src/gui/mac/WindowClasses/HYPlatformTreePanel.cpp
hyphy-src/src/gui/mac/include/HYPlatformButtonMenu.h
hyphy-src/src/gui/mac/include/HYPlatformComponent.h
hyphy-src/src/gui/mac/include/HYPlatformGraphicPane.h
hyphy-src/src/gui/mac/include/HYPlatformWindow.h
hyphy-src/src/gui/mac/include/Components/HYPlatformButton.h
hyphy-src/src/gui/mac/include/Components/HYPlatformButtonBar.h
hyphy-src/src/gui/mac/include/Components/HYPlatformCheckbox.h
hyphy-src/src/gui/mac/include/Components/HYPlatformLabel.h
hyphy-src/src/gui/mac/include/Components/HYPlatformList.h
hyphy-src/src/gui/mac/include/Components/HYPlatformPullDown.h
hyphy-src/src/gui/mac/include/Components/HYPlatformTable.h
hyphy-src/src/gui/mac/include/Components/HYPlatformTextbox.h
hyphy-src/src/gui/qt/helpers.cpp
hyphy-src/src/gui/qt/hyphy_qt_utility.cpp
hyphy-src/src/gui/qt/hyphyevents.cpp
hyphy-src/src/gui/qt/hyphyhierarchicalselector.cpp
hyphy-src/src/gui/qt/hyphymain.cpp
hyphy-src/src/gui/qt/hyphymessageoutput.cpp
hyphy-src/src/gui/qt/main.cpp
hyphy-src/src/gui/qt/qterminal.cpp
hyphy-src/src/gui/qt/simplerequest.cpp
hyphy-src/src/gui/qt/include/hyphy_qt_helpers.h
hyphy-src/src/gui/qt/include/hyphyevents.h
hyphy-src/src/gui/qt/include/hyphyhierarchicalselector.h
hyphy-src/src/gui/qt/include/hyphymain.h
hyphy-src/src/gui/qt/include/hyphymessageoutput.h
hyphy-src/src/gui/qt/include/qterminal.h
hyphy-src/src/gui/qt/include/simplerequest.h
hyphy-src/src/gui/qt/ui/hyphyhierarchicalselector.ui
hyphy-src/src/gui/qt/ui/hyphymain.ui
hyphy-src/src/gui/qt/ui/hyphymessageoutput.ui
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