MANIFEST.in
README
setup.py
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/Link/THyPhy.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/SWIGWrappers/THyPhy_python.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/contrib/SQLite-3.8.2/shell.c
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/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/_hyExecutionContext.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/alignment.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/avllist.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/avllistx.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/avllistxl.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/baseobj.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/batchlan.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/batchlan2.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/batchlanhelpers.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/batchlanruntime.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/calcnode.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/calcnode2.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/category.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/constant.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/error.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/fisher_exact.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/formula.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/fstring.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/likefunc.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/likefunc2.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/likefuncocl.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/list.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/mathobj.cpp
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/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/operation.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/parser.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/parser2.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/polynoml.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/regex.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/sequence.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/simplelist.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/site.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/stack.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/strings.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/trie.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/variable.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/core/variablecontainer.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/gui/preferences.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/new/bayesgraph.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/new/bayesgraph2.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/new/bgm.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/new/bgm2.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/work/hyphy-python-0.1.6/hyphy-src/src/new/scfg.cpp
/opt/conda/conda-bld/python-hyphy-python_1517851303209/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
hyphy-src/Examples/SimpleAnalyses/HKY85.bf
hyphy-src/Examples/SimpleAnalyses/HKY85shared.bf
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
hyphy-src/Examples/SimpleAnalyses/REVshared.bf
hyphy-src/Examples/SimpleAnalyses/data/hiv.nuc
hyphy-src/Examples/SimpleConstraints/F81K81uf_relratio.bf
hyphy-src/Examples/SimpleConstraints/F81relrate.bf
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
hyphy-src/contrib/SQLite-3.8.2/sqlite3.c
hyphy-src/contrib/SQLite-3.8.2/sqlite3.h
hyphy-src/contrib/SQLite-3.8.2/sqlite3ext.h
hyphy-src/contrib/gtest-1.7.0/CHANGES
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hyphy-src/contrib/gtest-1.7.0/CONTRIBUTORS
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hyphy-src/contrib/gtest-1.7.0/Makefile.in
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hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-tuple.h.pump
hyphy-src/contrib/gtest-1.7.0/include/gtest/internal/gtest-type-util.h
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hyphy-src/contrib/gtest-1.7.0/m4/lt~obsolete.m4
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hyphy-src/contrib/gtest-1.7.0/msvc/gtest_prod_test.vcproj
hyphy-src/contrib/gtest-1.7.0/msvc/gtest_unittest-md.vcproj
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hyphy-src/contrib/gtest-1.7.0/samples/sample1.cc
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
hyphy-src/contrib/gtest-1.7.0/samples/sample2.h
hyphy-src/contrib/gtest-1.7.0/samples/sample2_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample3-inl.h
hyphy-src/contrib/gtest-1.7.0/samples/sample3_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample4.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample4.h
hyphy-src/contrib/gtest-1.7.0/samples/sample4_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample5_unittest.cc
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hyphy-src/contrib/gtest-1.7.0/samples/sample8_unittest.cc
hyphy-src/contrib/gtest-1.7.0/samples/sample9_unittest.cc
hyphy-src/contrib/gtest-1.7.0/scripts/fuse_gtest_files.py
hyphy-src/contrib/gtest-1.7.0/scripts/gen_gtest_pred_impl.py
hyphy-src/contrib/gtest-1.7.0/scripts/gtest-config.in
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hyphy-src/contrib/gtest-1.7.0/src/gtest-all.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-death-test.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-filepath.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-internal-inl.h
hyphy-src/contrib/gtest-1.7.0/src/gtest-port.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest-printers.cc
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hyphy-src/contrib/gtest-1.7.0/src/gtest.cc
hyphy-src/contrib/gtest-1.7.0/src/gtest_main.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-death-test_ex_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-death-test_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-filepath_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-linked_ptr_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-listener_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-message_test.cc
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
hyphy-src/contrib/gtest-1.7.0/test/gtest-param-test_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-param-test_test.h
hyphy-src/contrib/gtest-1.7.0/test/gtest-port_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-printers_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest-test-part_test.cc
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
hyphy-src/contrib/gtest-1.7.0/test/gtest_all_test.cc
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
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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_filter_unittest_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_help_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_help_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_list_tests_unittest.py
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_premature_exit_test.cc
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hyphy-src/contrib/gtest-1.7.0/test/gtest_repeat_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_shuffle_test.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_shuffle_test_.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_sole_header_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_stress_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_test_utils.py
hyphy-src/contrib/gtest-1.7.0/test/gtest_throw_on_failure_ex_test.cc
hyphy-src/contrib/gtest-1.7.0/test/gtest_throw_on_failure_test.py
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hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
hyphy-src/res/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
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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
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hyphy-src/res/TemplateBatchFiles/TemplateModels/MGwAA.ibf
hyphy-src/res/TemplateBatchFiles/TemplateModels/MGwEX.ibf
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hyphy-src/res/TemplateBatchFiles/TemplateModels/NRM.mdl
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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
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hyphy-src/res/TemplateBatchFiles/TemplateModels/WAG_F.mdl
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hyphy-src/res/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
hyphy-src/res/TemplateBatchFiles/TemplateModels/custm4x4.mdl
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hyphy-src/res/TemplateBatchFiles/TemplateModels/rtREV.mdl
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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
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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
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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
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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
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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
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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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