Name		Name	Last commit message	Last commit date
Latest commit History 361 Commits
CompareResults		CompareResults
Dataset		Dataset
EIT		EIT
AminoAcidDict.py		AminoAcidDict.py
AminoAcidsDistUtilities.py		AminoAcidsDistUtilities.py
CollisionContext.py		CollisionContext.py
CollisionFactor.py		CollisionFactor.py
CovModel.py		CovModel.py
CovSEARD.py		CovSEARD.py
DataGenerationRegime.py		DataGenerationRegime.py
DataStruct.py		DataStruct.py
DifferentiableFunction.py		DifferentiableFunction.py
EndPointSampler.py		EndPointSampler.py
EuclideanDistanceForAminoAcids.xlsx		EuclideanDistanceForAminoAcids.xlsx
EventQueue.py		EventQueue.py
ExactInVarianceTestHMC.py		ExactInVarianceTestHMC.py
ExactInvarianceTest.py		ExactInvarianceTest.py
ExpectedCompleteReversibleModel.py		ExpectedCompleteReversibleModel.py
ExpectedCompleteReversibleModelBinaryFactors.py		ExpectedCompleteReversibleModelBinaryFactors.py
ExpectedCompleteReversibleObjective.py		ExpectedCompleteReversibleObjective.py
ExpectedCompleteReversibleObjectiveBackup.py		ExpectedCompleteReversibleObjectiveBackup.py
FullTrajectorGeneration.py		FullTrajectorGeneration.py
GammaDistFactor.py		GammaDistFactor.py
GammaDistFactorForExchangeCoef.py		GammaDistFactorForExchangeCoef.py
HMC.py		HMC.py
HardCodedDictionaryUtils.py		HardCodedDictionaryUtils.py
HardCodedSparseGraphDict.py		HardCodedSparseGraphDict.py
HardCodedSparseGraphGivenNStates.py		HardCodedSparseGraphGivenNStates.py
HardCodedSparseGraphgivenNStatesHMC.py		HardCodedSparseGraphgivenNStatesHMC.py
InitialCountFactor.py		InitialCountFactor.py
LocalRFRunner.py		LocalRFRunner.py
LocalRFSamplerForBinaryWeights.py		LocalRFSamplerForBinaryWeights.py
MCMCForOnlyNormalFactors.py		MCMCForOnlyNormalFactors.py
MCMCRunningRegime.py		MCMCRunningRegime.py
Main.py		Main.py
MainForAminoAcids.py		MainForAminoAcids.py
MainForNormal.py		MainForNormal.py
MultipleConvexCollisionSolver.py		MultipleConvexCollisionSolver.py
MultivariateNormalFactor.py		MultivariateNormalFactor.py
NormalFactor.py		NormalFactor.py
OptionClasses.py		OptionClasses.py
Path.py		Path.py
PathStatistics.py		PathStatistics.py
PhyloLocalRFMove.py		PhyloLocalRFMove.py
README.md		README.md
RateMtxExpectations.py		RateMtxExpectations.py
ReversibleRateMtx.py		ReversibleRateMtx.py
ReversibleRateMtxPiAndBinaryWeightsWithGraphicalStructure.py		ReversibleRateMtxPiAndBinaryWeightsWithGraphicalStructure.py
ReversibleRateMtxPiAndExchangeGTR.py		ReversibleRateMtxPiAndExchangeGTR.py
SimplePhyloModelHMC.py		SimplePhyloModelHMC.py
SimplePhyloModelMCMCSparseGraph.py		SimplePhyloModelMCMCSparseGraph.py
SimplePhyloModelMCMCSparseGraphFixStationaryDist.py		SimplePhyloModelMCMCSparseGraphFixStationaryDist.py
SimuSeq.py		SimuSeq.py
SojournTimeFactor.py		SojournTimeFactor.py
SojournTimeFactorWithoutPiEst.py		SojournTimeFactorWithoutPiEst.py
SojournTimeFactorWithoutPiEstWithBinaryFactors.py		SojournTimeFactorWithoutPiEstWithBinaryFactors.py
TestExpectedCompleteReversibleObjectiveAndHMC.py		TestExpectedCompleteReversibleObjectiveAndHMC.py
TestForwardAndEndPointSampler.py		TestForwardAndEndPointSampler.py
TrajectoryRay.py		TrajectoryRay.py
TransformAminoAcidsToIndexFromCSV.py		TransformAminoAcidsToIndexFromCSV.py
TransitionCountFactor.py		TransitionCountFactor.py
TransitionCountFactorWithoutPiEst.py		TransitionCountFactorWithoutPiEst.py
TransitionCountWithoutPiWithBinaryFactors.py		TransitionCountWithoutPiWithBinaryFactors.py
Utils.py		Utils.py
UtilsForCheckingGeneration.py		UtilsForCheckingGeneration.py
__init__.py		__init__.py
getBivariateFeatGradientIndex.py		getBivariateFeatGradientIndex.py

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