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README
setup.py
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HyPhy/__init__.py
Link/THyPhy.cpp
Link/THyPhy.h
SWIGWrappers/THyPhy_py3.cpp
SWIGWrappers/THyPhy_python.cpp
hyphy-src/.gitignore
hyphy-src/CMakeLists.txt
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hyphy-src/Examples/Categories/definitions+MLE.bf
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hyphy-src/Examples/Categories/definitions2.bf
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hyphy-src/Examples/ConstraintDefinition/ReplicateConstraint1.bf
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hyphy-src/installers/Mac/DMG.key
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hyphy-src/res/ChartAddIns/Approximate_CDF
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hyphy-src/res/DatapanelAddIns/Sequence Plot
hyphy-src/res/DatapanelAddIns/TBD/Character Plot By Sequence
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hyphy-src/res/GeneticCodes/Thraustochytrium_mtDNA.cod
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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
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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
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hyphy-src/res/TemplateBatchFiles/lib2014/models/codon/MG_REV.bf
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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
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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/build_mingw_MEGA.sh
hyphy-src/scripts/build_mingw_gui.sh
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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
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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
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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
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hyphy-src/src/core/include/list.h
hyphy-src/src/core/include/mathobj.h
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hyphy-src/src/core/include/mypthread.h
hyphy-src/src/core/include/operation.h
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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
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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
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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
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hyphy-src/src/gui/include/Components/HYCanvas.h
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hyphy-src/src/gui/include/Components/HYList.h
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hyphy-src/src/gui/mac/HYPHY.icns
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hyphy-src/src/gui/mac/HYPlatformGraphicPane.cpp
hyphy-src/src/gui/mac/HYPlatformUtils.cpp
hyphy-src/src/gui/mac/HYPlatformWindow.cpp
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hyphy-src/src/gui/mac/Info.plist
hyphy-src/src/gui/mac/hydialogs.cpp
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hyphy-src/src/gui/mac/plist.xml
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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
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hyphy-src/src/gui/mac/WindowClasses/HYPlatformChartWindow.cpp
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hyphy-src/src/gui/mac/WindowClasses/HYPlatformGWindow.cpp
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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
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hyphy-src/src/gui/mac/include/HYPlatformWindow.h
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hyphy-src/src/gui/mac/include/Components/HYPlatformCheckbox.h
hyphy-src/src/gui/mac/include/Components/HYPlatformLabel.h
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hyphy-src/src/gui/mac/include/Components/HYPlatformPullDown.h
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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
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