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Project: beast-mcmc (GitHub Link)
  • beast-mcmc-master
    • release_pibuss
      • common
        • README.txt
      • Windows
        • icons
          • PiBuss.ico
        • pibuss_launch4j.xml
      • Linux
        • icons
        • scripts
          • pibuss
      • Mac
        • icons
          • πBuss.icns
    • src
      • test
        • dr
          • integration
            • BEASTInputFile.java
            • PathSampling.java
          • multidimensionalscaling
            • MDSRotationTest.java
            • MDSTest.java
          • util
            • EuclideanTransformTest.java
            • LKJTransformTest.java
          • evolution
            • TreeMetricsTest.java
            • FilteredTreeTraitTest.java
          • distibutions
            • InvGammaTest.java
            • InverseGaussianDistributionTest.java
            • BifractionalDiffusionDensityTest.java
            • NormalDistributionTest.java
            • GammaDistributionTest.java
            • LogNormalDistributionTest.java
          • evomodel
            • treelikelihood
              • SequenceLikelihoodTest.java
              • LikelihoodTest.java
              • PMDTestProblem.java
              • NormalizedSequenceLikelihoodTest.java
              • AncestralStateTreeLikelihoodTest.java
              • AscertainmentCorrectedLikelihoodTest.java
            • alloppnet
              • speciation
                • AlloppSpeciesNetworkModelTEST.java
            • treedatalikelihood
              • hmc
                • DiffusionGradientTest.java
              • continuous
                • BranchSpecificGradientTest.java
                • cdi
                  • SafeMultivariateActualizedWithDriftIntegratorTest.java
                • RepeatedMeasureFactorTest.java
                • ContinuousTraitTest.java
                • ContinuousDataLikelihoodDelegateTest.java
            • substmodel
              • TwoStateOccupancyMarkovRewardsTest.java
              • ProductChainFrequencyModelTest.java
              • HKYTest.java
              • BinaryCovarionModelTest.java
              • SpecificEigendecompositionTest.java
              • TwoStateMarkovRewardsTest.java
              • TN93Test.java
              • StateHistoryTest.java
              • TwoStateCovarionModelTest.java
              • EigendecompositionTest.java
              • TwoPhaseModelTest.java
              • MsatSamplingTreeLikelihoodTest.java
              • AsymQuadTest.java
              • GeneralF81Test.java
              • CompleteHistorySimulatorTest.java
              • CodonPartitionedRobustCountingTest.java
              • GeneralSubstitutionModelTest.java
              • ProductChainSubstitutionModelTest.java
              • TimeIrreversibleTest.java
              • MsatFullLikelihoodTest.java
              • CovarionHKYTest.java
              • LinearBiasTest.java
              • MarkovJumpsSubstitutionModelTest.java
              • testNtdBMA.java
              • VariableBranchCompleteHistorySimulatorTest.java
            • operators
              • UniformIntegerOperatorTest.java
              • FNPRTest.java
              • ImportanceSubtreeSwapTestProblem.java
              • ImportancePruneAndRegraftTestProblem.java
              • ExchangeOperatorTest.java
              • NNITest.java
              • OperatorAssert.java
              • NarrowExchangeTest.java
              • GibbsSubtreeSwapTestProblem.java
            • arg
              • operators
                • ARGAddRemoveOperatorTest.java
            • coalescent
              • MultiEpochExponentialTest.java
              • VDdemographicFunctionTest.java
            • sitemodel
              • testGammaSiteBMA.java
            • branchratemodel
              • RandomLocalClockTestProblem.java
              • UncorrelatedRelaxedClockTest.java
              • StrictClockTest.java
            • speciation
              • RLYModelTest.java
              • YuleModelTest.java
              • YuleLikelihoodTest.java
              • BirthDeathSSLikelihoodTest.java
              • BirthDeathLikelihoodTest.java
          • math
            • ProcrustesTest.java
            • GeneralizedIntegerGammaTest.java
            • distributions
              • TransformedMultivariateDistributionTest.java
            • matrixAlgebra
              • missingData
                • MissingOpsTest.java
            • MarkovRewardCoreTest.java
            • UniformizedStateHistoryTest.java
            • KDEDistributionTest.java
            • MathTestCase.java
            • EmpiricalBayesPoissonSmootherTest.java
            • KroneckerOperationTest.java
          • inference
            • prior
              • LognormalPriorTest.java
            • mcmc
              • MCMCTest.java
            • trace
              • TraceCorrelationAssert.java
            • operators
              • RandomWalkOperatorTest.java
            • distribution
              • ExponentialTiltedStabledDistributionTest.java
              • DirichletProcessTest.java
            • model
              • VectorSliceParameterTest.java
              • CompoundEigenMatrixTest.java
            • CorrelationSymmetricMatrixTest.java
          • app
            • beagle
              • MarkovJumpsTest.java
              • TN93Test.java
              • TinyTest.java
              • AncestralStateBeagleTreeLikelihoodTest.java
              • HiddenMarkovRatesTest.java
            • beauti
              • BeautiTesterConfig.java
              • BeautiTester.java
          • calibration
            • TestCalibratedYuleModel.java
      • dr
        • xml
          • XMLModelCombiner.java
          • XMLSyntaxRule.java
          • XMLObject.java
          • AbstractXMLObjectParser.java
          • XMLDocumentationHandler.java
          • Check.java
          • XHTMLReport.java
          • StringAttributeRule.java
          • XMLModelIdentifiable.java
          • AttributesParser.java
          • XMLParseException.java
          • XMLParser.java
          • Reportable.java
          • PropertyParser.java
          • AttributeParser.java
          • ObjectNotFoundException.java
          • MarkdownDocumentationHandler.java
          • ElementRule.java
          • XMLModelFile.java
          • Spawnable.java
          • AndRule.java
          • Reference.java
          • AttributeRule.java
          • ContentRule.java
          • Report.java
          • WikiDocumentationHandler.java
          • XORRule.java
          • OrRule.java
          • UserInput.java
          • ObjectStore.java
          • ClassComparator.java
          • XMLObjectParser.java
          • unittest
            • BeastUnitTest.java
        • inferencexml
          • SignTransformParser.java
          • trace
            • AICMAnalysisParser.java
            • HarmonicMeanAnalysisParser.java
            • TraceAnalysisParser.java
            • ArithmeticMeanAnalysisParser.java
            • MarginalLikelihoodAnalysisParser.java
            • LogFileTraceExporterParser.java
          • loggers
            • LoggerParser.java
            • MLLoggerParser.java
            • ColumnsParser.java
          • operators
            • SwapOperatorParser.java
            • SimpleOperatorScheduleParser.java
            • HierarchicalBitFlipOperatorParser.java
            • UniformOperatorParser.java
            • MultivariateNormalGibbsOperatorParser.java
            • RandomWalkOperatorParser.java
            • TreeMaximizationOperatorParser.java
            • JointOperatorParser.java
            • SelectorOperatorParser.java
            • MVOUCovarianceOperatorParser.java
            • TeamOperatorParser.java
            • NegationOperatorParser.java
            • UpDownOperatorParser.java
            • MultipleRandomWalkIntegerOperatorParser.java
            • JointGibbsOperatorParser.java
            • SetOperatorParser.java
            • shrinkage
              • ShrinkageAugmentedGibbsOperatorParser.java
              • BayesianBridgeShrinkageOperatorParser.java
              • ShrinkageGibbsOperatorParser.java
            • RandomWalkIntegerOperatorParser.java
            • BitMoveOperatorParser.java
            • MaximizerWrtParameterOperatorParser.java
            • MaskMoveOperatorParser.java
            • TransformedRandomWalkOperatorParser.java
            • hmc
              • ZigZagOperatorParser.java
              • HamiltonianMonteCarloOperatorParser.java
              • ReflectiveHamiltonianMonteCarloOperatorParser.java
              • BouncyParticleOperatorParser.java
            • TwoPhaseOperatorParser.java
            • TransformedParameterRandomWalkOperatorParser.java
            • DeltaMixOperatorParser.java
            • ScaleOperatorParser.java
            • DirtyLikelihoodOperatorParser.java
            • UniformIntegerOperatorParser.java
            • AlternatingOperatorScheduleParser.java
            • FireParameterOperatorParser.java
            • CenteredScaleOperatorParser.java
            • ApplyOperatorParser.java
            • ApplyOperatorOnceParser.java
            • SwapParameterOperatorParser.java
            • DeltaExchangeOperatorParser.java
            • EllipticalSliceOperatorParser.java
            • InvariantOperatorParser.java
            • BitFlipOperatorParser.java
            • factorAnalysis
              • LoadingsSparsityOperatorParser.java
              • FactorIndependenceOperatorParser.java
              • LoadingsGibbsOperatorParser.java
              • LFMSplitMergeOperatorParser.java
              • LatentFactorLiabilityGibbsOperatorParser.java
              • LoadingsIndependenceOperatorParser.java
              • FactorOperatorParser.java
              • FactorGibbsOperatorParser.java
              • LatentFactorModelPrecisionGibbsOperatorParser.java
              • FactorRJMCMCOperatorParser.java
              • LFMTargetedSearchOperatorParser.java
            • BitSwapOperatorParser.java
            • ValuesPoolSwapOperatorParser.java
          • hmc
            • LoadingsTransformParser.java
            • CompoundGradientParser.java
            • SumDerivativeParser.java
            • GradientWrapperParser.java
            • NumericalHessianParser.java
            • HessianWrapperParser.java
            • PathGradientParser.java
            • LFMLoadingsPotentialDerivativeParser.java
            • NormalPotentialDerivativeParser.java
            • MaskedGradientParser.java
            • RotationTranslationMaskParser.java
            • LFMFactorPotentialDerivativeParser.java
          • glm
            • GeneralizedLinearModelParser.java
            • MultivariateOUModelParser.java
          • distribution
            • HierarchicalGraphLikelihoodParser.java
            • LocationScaleJeffreysPriorParser.java
            • IndependentInverseGammaDistributionModelParser.java
            • InverseGammaDistributionModelParser.java
            • TruncatedDistributionLikelihoodParser.java
            • InverseGaussianDistributionModelParser.java
            • EmpiricalDistributionLikelihoodParser.java
            • TwoPieceLocationScaleDistributionModelParser.java
            • RowDimensionPoissonPriorParser.java
            • RandomWalkModelParser.java
            • CachedDistributionLikelihoodParser.java
            • FactorTreeGibbsOperatorParser.java
            • WorkingPriorParsers.java
            • DeterminentalPointProcessPriorParser.java
            • OnePGammaDistributionModelParser.java
            • LogNormalDistributionModelParser.java
            • PoissonDistributionModelParser.java
            • ScaledBetaDistributionModelParser.java
            • DistributionLikelihoodParser.java
            • IndependentNormalDistributionModelParser.java
            • shrinkage
              • BayesianBridgeDistributionModelParser.java
              • BayesianBridgeLikelihoodParser.java
            • MixedDistributionLikelihoodParser.java
            • RowDimensionMultinomialPriorParser.java
            • BetaDistributionModelParser.java
            • CompoundGaussianProcessParser.java
            • BinomialLikelihoodParser.java
            • GammaDistributionModelParser.java
            • MultivariateOUModel.java
            • PriorParsers.java
            • TDistributionModelParser.java
            • UniformDistributionModelParser.java
            • MultivariateNormalDistributionModelParser.java
            • DirichletProcessLikelihoodParser.java
            • ExponentialMarkovModelParser.java
            • TruncatedNormalDistributionModelParser.java
            • MomentDistributionModelParser.java
            • GeneralizedLinearModelParser.java
            • ModelSpecificPseudoPriorLikelihoodParser.java
            • RandomWalkGeneratorParser.java
            • TwoPartsDistributionLikelihoodParser.java
            • MultivariateOUModelParser.java
            • ExponentialDistributionModelParser.java
            • NormalDistributionModelParser.java
            • DistributionModelParser.java
            • SkewNormalDistributionModelParser.java
            • MarginalizedAlphaStableDistributionModelParser.java
            • NegativeBinomialDistributionModelParser.java
            • WishartGammaDistributionModelParser.java
          • MCMCParser.java
          • model
            • SumStatisticParser.java
            • CoulombPriorParser.java
            • TraitValidationProviderParser.java
            • DiagonalMatrixParser.java
            • ExpressionStatisticParser.java
            • NotBooleanStatisticParser.java
            • TransformedMultivariateParameterParser.java
            • ImmutableParameterParser.java
            • MaskedMatrixParameterParser.java
            • SumParameterParser.java
            • ThresholdStatisticParser.java
            • BlockUpperTriangularMatrixParameterParser.java
            • IndianBuffetProcessPriorParser.java
            • DummyLikelihoodParser.java
            • MatrixVectorProductParameterParser.java
            • CorrelationSymmetricMatrixParser.java
            • DiagonalContrainedMatrixViewParser.java
            • MarkovRandomFieldMatrixParser.java
            • MaskedParameterParser.java
            • CompoundParameterParser.java
            • CompoundLikelihoodParser.java
            • MatrixMatrixProductParser.java
            • JointParameterParser.java
            • OneOnXPriorParser.java
            • DifferenceMatrixParameterParser.java
            • OneOnX3PriorParser.java
            • DifferenceParameterParser.java
            • VarianceStatisticParser.java
            • ComplementParameterParser.java
            • ExponentialStatisticParser.java
            • DefaultModelParser.java
            • TransformedParameterParser.java
            • BooleanLikelihoodParser.java
            • TestStatisticParser.java
            • LikelihoodBenchmarkerParser.java
            • MeanStatisticParser.java
            • ProductStatisticParser.java
            • ScaleData.java
            • ElementWiseMatrixMultiplicationParser.java
            • DifferenceStatisticParser.java
            • NegativeStatisticParser.java
            • SubStatisticParser.java
            • RPNcalculatorStatisticParser.java
            • CrossValidatorParser.java
            • DuplicatedParameterParser.java
            • ReciprocalStatisticParser.java
            • FastBlockUpperTriangularMatrixParameterParser.java
            • RatioStatisticParser.java
            • NotStatisticParser.java
            • LogarithmStatisticParser.java
            • ThreadedCompoundLikelihoodParser.java
            • AdaptableSizeFastMatrixParameterParser.java
            • TraitValidationParser.java
            • CompoundSymmetricMatrixParser.java
            • ProductParameterParser.java
            • CachedMatrixInverseParser.java
            • LatentFactorModelParser.java
          • MLOptimizerParser.java
        • top-level-packages.txt
        • geo
          • GreatCircleDistances.java
          • GeoSpatialCollectionModel.java
          • RateMatrix.java
          • Polygon.java
          • GTOPO30Tile.java
          • ManyUniformGeoDistributionModelParser.java
          • BrownianBridge1D.java
          • Reject.java
          • Lattice.java
          • distributions
            • HyperSphereDistribution.java
            • VonMisesFisherDistribution.java
            • FisherBinghamKentDistribution.java
            • VonMisesDistribution.java
          • KMLRenderer.java
          • InhomogeneousRandomWalk.java
          • KernelDensityEstimator2D.java
          • NumericalSpaceTimeProbs2D.java
          • MultivariateBrownianBridge.java
          • GTOPO30Panel.java
          • SpaceTimeRejector1D.java
          • operators
            • UniformGeoSpatialOperatorParser.java
            • UniformGeoSpatialOperator.java
          • GTOPO30RandomWalk.java
          • VisualizeBrownianBridge2D.java
          • testGreatCircleDistances.xml
          • IslandLattice.java
          • Location.java
          • NewPolygon2D.java
          • VisualizeSpaceTimeSim2D.java
          • SpaceTime.java
          • KMLViewer.java
          • KMLCoordinates.java
          • Polygon2DSampling.java
          • ManyUniformGeoDistributionModel.java
          • contouring
            • ContourGenerator.java
            • ContourMode.java
            • ContourWithSynder.java
            • SnyderContour.java
            • ContourWithR.java
            • ContourMaker.java
            • ContourPath.java
            • ContourAttrib.java
          • color
            • ColorScheme.java
            • ChannelColorScheme.java
          • MultiRegionGeoSpatialDistribution.java
          • AbstractPolygon2D.java
          • GeoSpatialDistribution.java
          • SpaceTimeRejector.java
          • math
            • SphericalPolarCoordinates.java
            • Vector3D.java
            • Space.java
          • ViewTransform.java
          • VisualizeKMLBrownianBridge.java
          • testLocations.xml
          • Polygon2DFactory.java
          • cartogram
            • CartogramMapping.java
          • GTOPO30Browser.java
          • Polygon2D.java
          • SpaceTimeSimulator.java
          • VisualizeKMLJointProb.java
          • VisualizeKMLNumericalProbs.java
        • util
          • CommonCitations.java
          • Keywordable.java
          • CorrelationToCholesky.java
          • TabularData.java
          • Property.java
          • TIFFWriter.java
          • EuclideanToInfiniteNormUnitBallTransform.java
          • Citable.java
          • Attributable.java
          • DataTable.java
          • Citation.java
          • MergeSort.java
          • LKJCholeskyTransformConstrainedWithDiag.java
          • StopWatch.java
          • PositiveOrderedTransform.java
          • XHTMLable.java
          • TaskListener.java
          • Attribute.java
          • Identifiable.java
          • Timer.java
          • EuclideanBallToRTransform.java
          • TransformParsers.java
          • Version.java
          • ComparableDouble.java
          • Author.java
          • LKJTransformParser.java
          • MessageLogHandler.java
          • FileHelpers.java
          • LKJTransformConstrained.java
          • HeapSort.java
          • ErrorLogHandler.java
          • LKJCholeskyTransformConstrained.java
          • Pair.java
          • NumberFormatter.java
          • FrequencyDistribution.java
          • Transform.java
          • Permutator.java
          • FrequencySet.java
          • HTMLOutput.java
        • oldevomodelxml
          • treelikelihood
            • TreeLikelihoodParser.java
            • AncestralStateTreeLikelihoodParser.java
            • MicrosatelliteSamplerTreeLikelihoodParser.java
            • HiddenLinkageLikelihoodParser.java
            • MarkovJumpsTreeLikelihoodParser.java
          • MSSD
            • SingleTipObservationProcessParser.java
            • AnyTipObservationProcessParser.java
            • ALSSiteModelParser.java
            • ExponentialBranchLengthTreePriorParser.java
            • ALSTreeLikelihoodParser.java
          • substmodel
            • GeneralSubstitutionModelParser.java
            • YangCodonModelParser.java
            • EmpiricalCodonModelParser.java
            • TN93Parser.java
            • NtdBMAParser.java
            • FrequencyModelParser.java
            • CovarionGTRParser.java
            • GLMSubstitutionModelParser.java
            • LinearBiasModelParser.java
            • CovarionHKYParser.java
            • NewMicrosatelliteModelParser.java
            • PCACodonModelParser.java
            • BinarySubstitutionModelParser.java
            • TwoStateCovarionModelParser.java
            • BinaryCovarionModelParser.java
            • HKYParser.java
            • ComplexSubstitutionModelParser.java
            • MutationDeathModelParser.java
            • GeneralF81ModelParser.java
            • MsatBMAParser.java
            • AsymQuadModelParser.java
            • EmpiricalAminoAcidModelParser.java
            • SubstitutionEpochModelParser.java
            • TwoPhaseModelParser.java
            • PositiveDefiniteSubstitutionModelParser.java
            • MkModelParser.java
            • LewisMkSubstitutionModelParser.java
            • GTRParser.java
          • clock
            • UCLikelihoodParser.java
            • ACLikelihoodParser.java
          • indel
            • TKF91ModelParser.java
            • IstvanOperatorParser.java
            • TKF91LikelihoodParser.java
          • sitemodel
            • SampleStateAndCategoryModelParser.java
            • SampleQuantileLociRatesParser.java
            • GammaSiteModelParser.java
            • SampleStateModelParser.java
            • DiscretizedLociRatesParser.java
            • CategorySiteModelParser.java
            • GammaSiteBMAParser.java
        • evolution
          • colouring
            • TreeColouring.java
            • ColourChangeMatrix.java
            • BranchColouring.java
            • ColourSampler.java
            • StructuredColourSampler.java
            • TreeColouringProvider.java
            • DefaultBranchColouring.java
            • DefaultTreeColouring.java
            • BasicColourSampler.java
            • SubstitutionModelToColourChangeMatrix.java
            • TwoColourSampler.java
          • wrightfisher
            • SimpleMutator.java
            • GammaFitnessFunction.java
            • Genome.java
            • BakSneppenFitness.java
            • SimpleGenome.java
            • FitnessFunction.java
            • SelectionMapping.java
            • Population.java
            • EmpiricalFitnessFunction.java
            • CodonFitnessFunction.java
            • BinaryMutator.java
            • Mutator.java
            • NeutralModel.java
            • Mutation.java
            • GammaInvFitnessFunction.java
          • MetagenomeData.java
          • util
            • Taxa.java
            • MutableTaxonList.java
            • TimeScale.java
            • TaxonList.java
            • Units.java
            • Location.java
            • Date.java
            • MutableTaxonListListener.java
            • Taxon.java
          • datatype
            • DataType.java
            • HiddenNucleotides.java
            • AminoAcids.java
            • PairedDataType.java
            • Codons.java
            • GeneticCode.java
            • MutationDeathType.java
            • SimpleCodons.java
            • Microsatellite.java
            • CodonTable.java
            • P2P.java
            • HiddenCodons.java
            • HiddenDataType.java
            • Nucleotides.java
            • ContinuousDataType.java
            • GeneralDataType.java
            • TwoStates.java
            • HiddenAminoAcids.java
            • TwoStateCovarion.java
            • OldHiddenNucleotides.java
            • PloidyType.java
          • alignment
            • Patterns.java
            • WrappedAlignment.java
            • PairedSitePatterns.java
            • JackknifePatterns.java
            • AscertainedSitePatterns.java
            • ExtractPairs.java
            • SiteList.java
            • GapStrippedAlignment.java
            • ShuffledSiteList.java
            • Defects.java
            • UncertainSiteList.java
            • PatternList.java
            • HypermutantAlignment.java
            • Alignment.java
            • GapUtils.java
            • SitePatterns.java
            • ResamplePatterns.java
            • ConvertAlignment.java
            • Consensus.java
            • MicrosatellitePatternStatistic.java
            • AlignmentParseException.java
            • BootstrapPatterns.java
            • CharSetAlignment.java
            • SimpleSiteList.java
            • SimpleAlignment.java
          • continuous
            • Contrastable.java
            • Continuous.java
            • ContinuousTraitLikelihood.java
            • DiffusionLikelihood.java
          • sequence
            • Sequence.java
            • Sequences.java
            • SequenceList.java
            • UncertainSequence.java
          • coalescent
            • ScaledDemographic.java
            • ExponentialGrowth.java
            • ConstantPopulation.java
            • MultiEpochExponential.java
            • CataclysmicDemographic.java
            • PiecewiseLinearPopulation.java
            • Intervals.java
            • CoalescentSimulator.java
            • PiecewiseConstantPopulation.java
            • ExpConstExpDemographic.java
            • ConstExponential.java
            • Expansion.java
            • ExpConstant.java
            • TwoEpochDemographic.java
            • ExponentialExponential.java
            • IntervalType.java
            • PLCoalescentSimulator.java
            • ConstLogistic.java
            • structure
              • StructuredCoalescentSimulator.java
              • StructuredIntervalList.java
              • Event.java
              • ColouredTreeIntervals.java
              • StructuredCoalescent.java
              • MetaPopulation.java
            • Skyline.java
            • LinearGrowth.java
            • PiecewiseExponentialPopulation.java
            • ExponentialBSPGrowth.java
            • FlexibleGrowth.java
            • IntervalList.java
            • EmpiricalPiecewiseConstant.java
            • LogisticGrowth.java
            • PowerLawGrowth.java
            • DemographicFunction.java
            • ConstExpConst.java
            • Coalescent.java
            • TreeIntervals.java
            • ExponentialSawtooth.java
            • ExponentialLogistic.java
          • parsimony
            • SankoffParsimony.java
            • ParsimonyCriterion.java
            • FitchParsimony.java
            • Parsimony.java
            • TestParsimony.java
          • io
            • NexusImporter.java
            • NewickImporter.java
            • PatternImporter.java
            • FastaImporter.java
            • TreeImporter.java
            • MigrateTreeImporter.java
            • PhylipSequentialImporter.java
            • TreeTrace.java
            • SequenceImporter.java
            • TreeExporter.java
            • MicroSatImporter.java
            • Importer.java
          • tree
            • NodeRef.java
            • treemetrics
              • RootedBranchScoreMetric.java
              • BranchScoreMetric.java
              • TestTreeMetrics.java
              • KendallColijnPathDifferenceMetric.java
              • CladeHeightMetric.java
              • RobinsonFouldsMetric.java
              • SteelPennyPathDifferenceMetric.java
              • TreeMetric.java
            • CountConstrainedRankedHistories.java
            • UPGMATree.java
            • MutableTreeListener.java
            • TransformedTreeTraitProvider.java
            • CladeSet.java
            • Clade.java
            • CladeDistribution.java
            • BranchRates.java
            • CladeMetric.java
            • LeastSquaresClockTree.java
            • RzhetskyNeiBranchLengthsTree.java
            • MutableTreeModel.java
            • RateSmoothingTree.java
            • TestTreeUtils.java
            • TreeTraitProvider.java
            • TreeMetrics.java
            • SplitSystem.java
            • TransformableTree.java
            • Tree.java
            • TreeTrait.java
            • TreeNodeFilter.java
            • SubtreeSlide.java
            • TreeAttributeProvider.java
            • UnrootedTree.java
            • ClusteringTree.java
            • TreeShape.java
            • FlexibleNode.java
            • RankedForest.java
            • ColouredTree.java
            • SimpleNode.java
            • RankedNode.java
            • MutableTree.java
            • MutableTreeUtils.java
            • SplitUtils.java
            • SimpleTree.java
            • ImportanceDistribution.java
            • ColourChange.java
            • FlexibleTree.java
            • LineageCountThroughTime.java
            • NeighborJoiningTree.java
            • TreeDoubleTraitProvider.java
            • TreeUtils.java
          • LinkedGroup.java
          • phylogeny
            • Lineage.java
            • Phylogeny.java
          • LinkageConstraints.java
          • distance
            • DistanceMatrix.java
            • JukesCantorDistanceMatrix.java
            • PatristicDistanceMatrix.java
            • SMMDistanceMatrix.java
            • F84DistanceMatrix.java
        • evomodel
          • branchmodel
            • ArbitrarySubstitutionParameterBranchModel.java
            • HomogeneousBranchModel.java
            • ExternalInternalBranchModel.java
            • EpochBranchModel.java
            • BranchAssignmentModel.java
            • BranchSpecificBranchModel.java
            • lineagespecific
              • DirichletProcessPriorParser.java
              • BeagleBranchLikelihoodParser.java
              • LineageSpecificBranchModel.java
              • DirichletProcessPriorLogger.java
              • CountableRealizationsParameter.java
              • RatioParameter.java
              • RatioParameterParser.java
              • LineageSpecificBranchModelParser.java
              • DirichletProcessPriorLoggerParser.java
              • DirichletProcessPrior.java
              • BranchSpecificTrait.java
              • CountableRealizationsParameterParser.java
              • BranchLikelihood.java
              • BeagleBranchLikelihood.java
              • DirichletProcessOperator.java
              • DirichletProcessOperatorParser.java
              • BranchSpecificTraitParser.java
            • BranchSpecificSubstitutionParameterBranchModel.java
            • BranchModel.java
            • RandomBranchModel.java
            • RandomBranchAssignmentModel.java
          • treelikelihood
            • MultiPartitionTreeLikelihood.java
            • ApproximatePoissonTreeLikelihood.java
            • AbstractTreeLikelihood.java
            • LikelihoodScalingProvider.java
            • AncestralStateBeagleTreeLikelihood.java
            • LikelihoodPartialsProvider.java
            • AbstractSinglePartitionTreeLikelihood.java
            • SubstitutionModelDelegate.java
            • BeagleOperationReport.java
            • MarkovJumpsTraitProvider.java
            • EvolutionaryProcessDelegate.java
            • SplitBySiteTraitLogger.java
            • PartialsRescalingScheme.java
            • MarkovJumpsBeagleTreeLikelihood.java
            • BeagleTreeLikelihood.java
            • AncestralStateTraitProvider.java
            • utilities
              • ModelExtensionTraitLogger.java
              • CompleteHistoryLogger.java
              • TreeTraitLogger.java
              • DnDsLogger.java
              • HistoryFilter.java
          • MSSD
            • AnyTipObservationProcess.java
            • AbstractObservationProcess.java
            • ALSBeagleTreeLikelihood.java
            • SingleTipObservationProcess.java
          • alloppnet
            • parsers
              • AlloppSpeciesNetworkModelParser.java
              • AlloppMoveLegsParser.java
              • AlloppNumHybsStatisticParser.java
              • BirthDeathCollapseNClustersStatisticParser.java
              • AlloppSpeciesBindingsApSpInfoParser.java
              • AlloppMSCoalescentParser.java
              • MulTreeSequenceReassignmentParser.java
              • AlloppChangeNumHybridizationsParser.java
              • BirthDeathCollapseModelParser.java
              • MulTreeNodeSlideParser.java
              • AlloppSequenceReassignmentParser.java
              • AlloppSpeciesBindingsParser.java
              • MulSpeciesTreePriorParser.java
              • AlloppHybPopSizesScaleParser.java
              • MulSpeciesBindingsParser.java
              • AlloppNetworkNodeSlideParser.java
              • AlloppSpeciesBindingsIndividualParser.java
              • MulSpeciesTreeModelParser.java
              • MulMSCoalescentParser.java
              • AlloppNetworkPriorParser.java
              • AlloppNetworkPriorModelParser.java
            • util
              • AlloppMisc.java
            • operators
              • AlloppSequenceReassignment.java
              • AlloppNetworkNodeSlide.java
              • MulTreeSequenceReassignment.java
              • AlloppMoveLegs.java
              • MulTreeNodeSlide.java
              • AlloppChangeNumHybridizations.java
              • AlloppHybPopSizesScale.java
            • package-info.java
            • tree
              • SlidableTree.java
            • speciation
              • AlloppSpeciesBindings.java
              • AlloppNode.java
              • AlloppDiploidHistory.java
              • AlloppMulLabTree.java
              • MulSpeciesTreeModel.java
              • BirthDeathCollapseNClustersStatistic.java
              • AlloppNetworkPriorModel.java
              • MulMSCoalescent.java
              • MulSpeciesBindings.java
              • AlloppMSCoalescent.java
              • BirthDeathCollapseModel.java
              • AlloppLeggedTree.java
              • MulSpeciesTreePrior.java
              • AlloppSpeciesNetworkModel.java
              • AlloppNetworkPrior.java
              • AlloppNumHybsStatistic.java
          • tipstatesmodel
            • HypermutantErrorModel.java
            • SequenceErrorModel.java
            • TipStatesModel.java
          • treedatalikelihood
            • BeagleFunctionality.java
            • LikelihoodTreeTraversal.java
            • HomogenousSubstitutionModelDelegate.java
            • MultiPartitionDataLikelihoodDelegate.java
            • discrete
              • NodeHeightToRatiosFullTransformDelegate.java
              • BranchSubstitutionParameterScaleGradient.java
              • BranchSubstitutionParameterGradient.java
              • BranchDifferentialMassProvider.java
              • NodeHeightTransformTest.java
              • LocationGradient.java
              • DiscreteTraitBranchRateGradient.java
              • NodeHeightToCoalescentIntervalsDelegate.java
              • NodeHeightGradientForDiscreteTrait.java
              • HyperParameterBranchRateGradient.java
              • MaximizerWrtParameter.java
              • HyperParameterBranchSubstitutionParameterGradient.java
              • ScaleGradient.java
              • NewLocationGradient.java
              • BranchSubstitutionParameterDelegate.java
              • AbstractNodeHeightTransformDelegate.java
              • BranchRateGradientForDiscreteTrait.java
              • NodeHeightProxyParameter.java
              • NodeHeightToRatiosTransformDelegate.java
              • HyperParameterGradient.java
              • DiscreteTraitBranchRateDelegate.java
              • NodeHeightTransform.java
              • BranchSubstitutionParameterLocationGradient.java
              • NodeHeightBounds.java
              • LocalBranchRateGradientForDiscreteTrait.java
            • BufferIndexHelper.java
            • ProcessSimulation.java
            • BeagleDataLikelihoodDelegate.java
            • preorder
              • MatrixSufficientStatistics.java
              • BranchConditionalDistributionDelegate.java
              • BranchSufficientStatistics.java
              • ConditionalVarianceAndTransform2.java
              • ConditionalVarianceAndTransform.java
              • ConditionalPrecisionAndTransform2.java
              • WrappedNormalSufficientStatistics.java
              • TipFullConditionalDistributionDelegate.java
              • NewTipFullConditionalDistributionDelegate.java
              • WrappedTipFullConditionalDistributionDelegate.java
              • NormalSufficientStatistics.java
              • ConditionalOnTipsRealizedDelegate.java
              • AbstractFullConditionalDistributionDelegate.java
              • TipGradientViaFullConditionalDelegate.java
              • UnconditionalOnTipsDelegate.java
              • ModelExtensionProvider.java
              • LocalBranchRateDelegate.java
              • TipRealizedValuesViaFullConditionalDelegate.java
              • ContinuousExtensionDelegate.java
              • ProcessSimulationDelegate.java
              • AbstractRealizedContinuousTraitDelegate.java
              • AbstractValuesViaFullConditionalDelegate.java
              • AbstractDiscreteTraitDelegate.java
              • ConditionalPrecisionAndTransform.java
              • MultivariateConditionalOnTipsRealizedDelegate.java
            • DataLikelihoodTester2.java
            • RateRescalingScheme.java
            • TreeDataLikelihood.java
            • TreeTraversal.java
            • SubstitutionModelDelegate.java
            • DataLikelihoodTester.java
            • SimulationTreeTraversal.java
            • hmc
              • PrecisionGradient.java
              • DiagonalPrecisionGradient.java
              • GradientWrtPrecisionProvider.java
              • MultivariateChainRule.java
              • CorrelationPrecisionGradient.java
              • AbstractPrecisionGradient.java
              • DiffusionParametersGradient.java
              • AbstractDiffusionGradient.java
            • continuous
              • AbstractDiffusionModelDelegate.java
              • OUDiffusionModelDelegate.java
              • cdi
                • PrecisionType.java
                • InstanceDetails.java
                • ContinuousDiffusionIntegrator.java
                • CDIException.java
                • CDIJNIWrapper.java
                • CDIErrorCode.java
                • MultivariateIntegrator.java
                • SafeMultivariateDiagonalActualizedWithDriftIntegrator.java
                • ResourceDetails.java
                • SafeMultivariateWithDriftIntegrator.java
                • CDIFactory.java
                • CDIFlag.java
                • SafeMultivariateIntegrator.java
                • DriftType.java
                • SafeMultivariateActualizedWithDriftIntegrator.java
              • BranchRateGradient.java
              • PartiallyMissingInformation.java
              • TreeTipGaussianProcess.java
              • RootProcessDelegate.java
              • IntegratedFactorAnalysisLikelihood.java
              • EmptyTraitDataModel.java
              • ContinuousTraitDataModel.java
              • MultivariateTraitDebugUtilities.java
              • ContinuousTraitPartialsProvider.java
              • WishartStatisticsWrapper.java
              • RepeatedMeasuresTraitDataModel.java
              • IntegratedOUDiffusionModelDelegate.java
              • RepeatedMeasuresWishartStatistics.java
              • DiffusionProcessDelegate.java
              • BranchSpecificGradient.java
              • ConjugateRootTraitPrior.java
              • DriftDiffusionModelDelegate.java
              • ContinuousTraitGradientForBranch.java
              • HomogeneousDiffusionModelDelegate.java
              • AbstractDriftDiffusionModelDelegate.java
              • ElementaryVectorDataModel.java
              • ContinuousDataLikelihoodDelegate.java
              • IntegratedProcessTraitDataModel.java
              • ContinuousRateTransformation.java
              • TreeTipGradient.java
            • EvolutionaryProcessDelegate.java
            • DataLikelihoodDelegate.java
            • PreOrderSettings.java
            • ProcessOnTreeDelegate.java
          • substmodel
            • DifferentiableSubstitutionModel.java
            • PCARateMatrixMammalia.java
            • BranchSpecificSubstitutionModelProvider.java
            • EmpiricalRateMatrixReader.java
            • GeneralSubstitutionModel.java
            • CodonLabeling.java
            • ComplexColtEigenSystem.java
            • AbstractCovarionModel.java
            • CodonPartitionedRobustCounting.java
            • StratifiedTraitOutputFormat.java
            • ComplexSubstitutionModel.java
            • CovarionFrequencyModel.java
            • CodonFromNucleotideFrequencyModel.java
            • MutationDeathModel.java
            • UniformizedSubstitutionModel.java
            • nucleotide
              • GTR.java
              • TN93.java
              • NucModelType.java
              • HKY.java
            • OldGLMSubstitutionModel.java
            • FrequencyModel.java
            • MarkovModulatedSubstitutionModel.java
            • DifferentiableSubstitutionModelUtil.java
            • ProductChainFrequencyModel.java
            • SubstitutionProcess.java
            • SVSGeneralSubstitutionModel.java
            • EigenDecomposition.java
            • DependentProductChainSubstitutionModel.java
            • MarkovModulatedFrequencyModel.java
            • EigenSystem.java
            • EmpiricalRateMatrix.java
            • ProductChainSubstitutionModel.java
            • MarkovJumpsSubstitutionModel.java
            • ExposeRateCategoriesWrapper.java
            • DefaultEigenSystem.java
            • codon
              • AbstractCodonModel.java
              • CodonOptions.java
              • MarkovModulatedGY94CodonModel.java
              • GY94CodonModel.java
              • PCACodonModel.java
              • MG94HKYCodonModel.java
              • MG94K80CodonModel.java
              • EmpiricalCodonModel.java
            • DifferentialUtils.java
            • SVSComplexSubstitutionModel.java
            • DifferentialMassProvider.java
            • AbstractPCARateMatrix.java
            • BinaryCovarionModel.java
            • ColtEigenSystem.java
            • aminoacid
              • LG.java
              • JTT.java
              • Blosum62.java
              • MTREV.java
              • WAG.java
              • AminoAcidModelType.java
              • FLU.java
              • CPREV.java
              • EmpiricalAminoAcidModel.java
              • Dayhoff.java
            • GLMSubstitutionModel.java
            • ParameterReplaceableSubstitutionModel.java
            • SubstitutionModel.java
            • BaseSubstitutionModel.java
          • trace
            • CnCsPerSiteAnalysis.java
            • OldDnDsPerSiteAnalysis.java
            • CnCsToDnDsPerSiteAnalysis.java
            • DnDsPerSiteAnalysis.java
          • operators
            • AbstractTreeOperator.java
            • TreeNodeSlide.java
            • SubtreeSlideOperator.java
            • AbstractImportanceDistributionOperator.java
            • FNPR.java
            • OldLatentLiabilityGibbsOperator.java
            • RateExchangeOperator.java
            • FixedHeightSubtreePruneRegraftOperator.java
            • GibbsSubtreeSwap.java
            • MicrosatelliteUpDownOperator.java
            • ExchangeOperator.java
            • PrecisionMatrixGibbsOperator.java
            • RateScaleOperator.java
            • RandomWalkIntegerSetSizeWeightedOperator.java
            • MicrosatelliteFullAncestryImportanceSamplingOperator.java
            • MicrosatelliteSingleAncestralStateGibbsOperator.java
            • TipTraitSwapOperator.java
            • RLCNarrowExchangeOperator.java
            • CCPImportanceDistributionOperator.java
            • RandomWalkOnMapOperator.java
            • SubtreeJumpOperator.java
            • MoveLinkageGroup.java
            • ImportanceSubtreeSwap.java
            • TipStateSwapOperator.java
            • FunkyPriorMixerOperator.java
            • RateSampleOperator.java
            • TreeBitRandomWalkOperator.java
            • MicrosatelliteBitFlipOperator.java
            • NewLatentLiabilityGibbs.java
            • CategoryOperator.java
            • TraitRateGibbsOperator.java
            • LatentLiabilityGibbs.java
            • EmpiricalTreeDistributionOperator.java
            • CompoundPrecisionMatrixGibbsOperator.java
            • GibbsPruneAndRegraft.java
            • NodeHeightScaleOperator.java
            • WilsonBalding.java
            • PatternWeightIncrementOperator.java
            • TraitGibbsOperator.java
            • MicrosatelliteModelSelectOperator.java
            • ImportancePruneAndRegraft.java
            • DiscretizedLocationOperator.java
            • RandomWalkIntegerNodeHeightWeightedOperator.java
            • BitFlipInSubstitutionModelOperator.java
            • NNI.java
            • TreeUniform.java
            • AbstractAdaptableTreeOperator.java
            • CorrelationMatrixGibbsOperator.java
            • ImportanceNarrowExchange.java
            • RateVarianceScaleOperator.java
            • LinkageGroupSwap.java
            • TreeBitMoveOperator.java
            • SubtreeLeapOperator.java
          • arg
            • ARGTrace.java
            • ARGTreeLogger.java
            • ARGReassortmentTimingStatistic.java
            • PoissonPartitionLikelihood.java
            • HierarchicalPartitionLikelihood.java
            • UniformPartitionLikelihood.java
            • ARGTree.java
            • ARGRelaxedClock.java
            • OldTreeLogger.java
            • RecombinationPartitionStatistic.java
            • ARGDistinctTreeCountStatistic.java
            • operators
              • SlidingPatternsOperator.java
              • ARGExchangeOperator.java
              • NonContiguousPartitionsException.java
              • ARGPartitioningOperator.java
              • ARGSubtreeSlideOperator.java
              • ARGOperatorFailedException.java
              • ARGAddRemoveEventOperator.java
              • ObsoleteARGAddRemoveEventOperator.java
              • ARGSwapOperator.java
              • ObsoleteARGNewEventOperator.java
              • ARGReassortmentOperator.java
            • ARGRatePrior.java
            • ARGTraceAnalysisParser.java
            • coalescent
              • ARGCoalescentLikelihood.java
              • ARGUniformPrior.java
              • VeryOldCoalescentLikelihood.java
            • ARGLogger.java
            • ARGModel.java
            • ARGPartitionLikelihood.java
            • parsers.txt
            • ARGTraceAnalysis.java
            • branchratemodel
              • ARGDiscretizedBranchRates.java
            • ARGReassortmentNodeCountStatistic.java
            • likelihood
              • ARGLikelihood.java
              • AbstractARGLikelihood.java
            • beast.properties
            • ARGTotalLengthStatistic.java
          • continuous
            • TreeDataContinuousDiffusionStatistic.java
            • InhibitionAssayLikelihood.java
            • SemiConjugateMultivariateTraitLikelihood.java
            • RestrictedPartialsModel.java
            • RootTraitMLE.java
            • MultinomialLatentLiabilityLikelihood.java
            • IntervalLatentLiabilityLikelihood.java
            • MixtureCartogramDiffusionModel.java
            • IndependentCoalescentSampler.java
            • MultivariateElasticModel.java
            • ConstrainedGaussianProcessRandomGenerator.java
            • CartogramDiffusionModel.java
            • ContinuousDiffusionStatistic.java
            • BifractionalDiffusionModel.java
            • OrderedLatentLiabilityLikelihood.java
            • DummyLatentTruncationProvider.java
            • ApproximateFactorAnalysisPrecisionMatrix.java
            • BivariateDiscreteDiffusionModel.java
            • FullyConjugateMultivariateTraitLikelihood.java
            • GibbsSampleFromTreeInterface.java
            • MultivariateDiffusionModel.java
            • BranchMagnitudeAttributeProvider.java
            • MapDiffusionModel.java
            • GibbsIndependentCoalescentOperator.java
            • plink
              • PlinkImporter.java
            • TraitLikelihood.java
            • SampledMultivariateTraitLikelihood.java
            • MissingInjection.java
            • MissingTraits.java
            • StandardizeTraits.java
            • hmc
              • IntegratedLoadingsGradient.java
              • LinearOrderTreePrecisionTraitProductProvider.java
              • FullyConjugateTreeTipsPotentialDerivative.java
              • TreeKroneckerPrecisionColumnProvider.java
              • CubicOrderTreePrecisionTraitProductProvider.java
              • TreePrecisionColumnProvider.java
              • TreePrecisionTraitProductProvider.java
              • OldLinearOrderTreePrecisionTraitProductProvider.java
              • TaxonTaskPool.java
            • TreeTraitSimulator.java
            • SimulateTrait.java
            • BinaryLatentLiabilityLikelihood.java
            • DiffusionRateCovarianceStatistic.java
            • GaussianProcessFromTree.java
            • NonPhylogeneticMultivariateTraitLikelihood.java
            • BivariateTraitBranchAttributeProvider.java
            • TopographicalMap.java
            • AbstractMultivariateTraitLikelihood.java
            • GibbsSampleMissingTraitsOperator.java
            • SoftThresholdLikelihood.java
            • VonMisesFisherDiffusionModel.java
            • TruncatedWorkingDistribution.java
            • StochasticDifferentialEquationModel.java
            • TreeTraitNormalDistributionModel.java
            • MultivariateTDiffusionModel.java
            • BranchDirectionAttributeProvider.java
            • LatentTruncation.java
            • BiasedMultivariateDiffusionModel.java
            • AncestralTaxonInTree.java
            • RestrictedPartials.java
            • DiffusionRateStatistic.java
            • MultivariateTraitUtils.java
            • IntegratedMultivariateTraitLikelihood.java
            • ContinuousLikelihood.java
            • RootTraitStatistic.java
            • GreatCircleDiffusionModel.java
            • MissingInjectionLogger.java
            • LatentFactorModelSimulator.java
            • DiffusionModel.java
          • transmission
            • TransmissionHistoryModel.java
            • TransmissionDemographicModel.java
            • TransmissionSimulator.java
            • TransmissionStatistic.java
            • HierarchicalTransmissionDemographicModel.java
            • TransmissionLikelihood.java
          • coalescent
            • MultiLociTreeSet.java
            • ConstantPopulationSizeModel.java
            • BayesianSkylineLikelihood.java
            • GMRFSkyrideGradient.java
            • CoalescentTreeIntervalStatistic.java
            • CoalescentEventsStatistic.java
            • GMRFFixedGridLikelihood.java
            • GMRFIntervalHeightsStatistic.java
            • CoalescentConstantLikelihood.java
            • OrnsteinUhlenbeckPriorLikelihood.java
            • GMRFMultilocusSkyrideLikelihood.java
            • GMRFDensityComponent.java
            • VDdemographicFunction.java
            • MultiTreeIntervals.java
            • VariableDemographicModel.java
            • SkylineLikelihood.java
            • LineageCountStatistic.java
            • demographicmodel
              • ExponentialGrowthModel.java
              • CataclysmicDemographicModel.java
              • ExponentialSawtoothModel.java
              • ExpConstExpDemographicModel.java
              • ConstExpConstModel.java
              • ConstantPopulationModel.java
              • ExpansionModel.java
              • LogisticGrowthModel.java
              • EmergingEpidemicModel.java
              • ExponentialExponentialModel.java
              • ConstantExponentialModel.java
              • EmpiricalPiecewiseModel.java
              • ExponentialLogisticModel.java
              • ExponentialConstantModel.java
              • PeakAndDeclineModel.java
              • ScaledPiecewiseModel.java
              • MultiEpochExponentialModel.java
              • AsymptoticGrowthModel.java
              • LinearGrowthModel.java
              • DemographicModel.java
              • PowerLawGrowthModel.java
              • ConstantLogisticModel.java
              • PiecewisePopulationModel.java
              • TwoEpochDemographicModel.java
            • PopulationSizeFunction.java
            • CoalescentSimulator.java
            • GMRFBivariateCurveAnalysis.java
            • PopulationSizeModel.java
            • basta
              • BeagleMatrixExponentiationDelegate.java
              • OldStructuredCoalescentLikelihood.java
              • BASTADensityTester.java
              • StructuredCoalescentLikelihood.java
              • StructuredCoalescentLikelihoodParser.java
            • GaussianProcessMultilocusSkytrackLikelihood.java
            • PopulationSizeGraph.java
            • CovariateGMRFSkylineLikelihood.java
            • CoalescentLikelihood.java
            • operators
              • GMRFMultilocusSkyrideBlockUpdateOperator.java
              • GaussianProcessSkytrackTreeOperator.java
              • SampleNonActiveGibbsOperator.java
              • GMRFSkyrideFixedEffectsGibbsOperator.java
              • GMRFSkyrideBlockUpdateOperator.java
              • GMRFSkygridBlockUpdateOperator.java
              • GaussianProcessSkytrackBlockUpdateOperator.java
              • BayesianSkylineGibbsOperator.java
            • hmc
              • GMRFGradient.java
            • ExponentialProductSufficientStatisticsLikelihood.java
            • structure
              • TreeColouringOperator.java
              • ConstantMigrationModel.java
              • MigrationModel.java
              • MetaPopulationModel.java
              • ColourSamplerModel.java
              • StructuredCoalescentLikelihood.java
            • OldAbstractCoalescentLikelihood.java
            • LogisticPopulationSizeModel.java
            • GMRFSkyrideLikelihood.java
            • AbstractCoalescentLikelihood.java
            • PiecewisePopulationSizeModel.java
            • VariableSkylineLikelihood.java
            • ExponentialProductPosteriorMeansLikelihood.java
            • GMRFTestLikelihood.java
            • GPSkytrackAnalysis.java
            • ExponentialProductLikelihood.java
            • PopSizeStatistic.java
            • OldGMRFSkyrideLikelihood.java
            • GaussianProcessSkytrackLikelihood.java
            • GaussianProcessSkytrackParser.java
            • BNPRSamplingLikelihood.java
            • ExponentialPopulationSizeModel.java
            • ExponentialSkythingLikelihood.java
            • BMPriorLikelihood.java
            • GMRFPopSizeStatistic.java
            • GammaProductLikelihood.java
            • CoalescentIntervalStatistic.java
            • TreeIntervals.java
            • GMRFSkygridLikelihood.java
            • CoalescentIntervalProvider.java
            • EBSPAnalysis.java
            • BayesianSkylinePopSizeStatistic.java
          • tree
            • TMRCAStatistic.java
            • HiddenLinkageModel.java
            • ParsimonyStateStatistic.java
            • TreeTransform.java
            • WanderingTaxonLogger.java
            • NodeTraitLogger.java
            • AncestralTrait.java
            • NodeHeightsStatistic.java
            • BackboneNodeFilter.java
            • RateStatistic.java
            • ExternalLengthStatistic.java
            • NewTreeModel.java
            • MonophylyStatistic.java
            • TreeParameterModel.java
            • MRCATraitStatistic.java
            • TransformedTreeTrait.java
            • HiddenLinkageLogger.java
            • MicrosatelliteSamplerTreeModel.java
            • TreeTraceAnalysis.java
            • ConditionalCladeProbability.java
            • TransformedTreeModel.java
            • AncestralTraitTreeModel.java
            • TipHeightLikelihood.java
            • HiddenLinkageTreeLogger.java
            • randomlocalmodel
              • RLTVLoggerOnTree.java
              • RandomLocalTreeVariable.java
              • RLTVLogger.java
              • RLTVAnalyzer.java
            • TrialTreeParameterModel.java
            • SpeciesTreeStatistic.java
            • ConvergenceLogger.java
            • OuScalarTreeTransform.java
            • TreeModel.java
            • ProgressiveScalarTreeTransform.java
            • ConditionalCladeFrequency.java
            • NewTreeParameterModel.java
            • StarTreeModel.java
            • TreeHeightStatistic.java
            • Convergence.java
            • TreeSummary.java
            • TerminalBranchStatistic.java
            • TreeChangedEvent.java
            • TreeMetricStatistic.java
            • TreeLogger.java
            • ParsimonyStatistic.java
            • UniformNodeHeightPrior.java
            • CTMCScalePrior.java
            • EmpiricalTreeDistributionModel.java
            • ConvergenceListener.java
            • AbstractCladeImportanceDistribution.java
            • RateCovarianceStatistic.java
            • MultivariateTreeParameterModel.java
            • TreeLengthStatistic.java
            • WeightedMultiplicativeBinary.java
            • TreeSpaceLogger.java
            • TreeStatistic.java
            • CompatibilityStatistic.java
            • SlicedMultivariateTreeParameterModel.java
            • SingleScalarTreeTransform.java
            • AbstractTreeParameterModel.java
            • TreeShapeStatistic.java
          • antigenic
            • AntigenicDriftPrior.java
            • ClusterSingleMoveOperator.java
            • DistanceDependentCRPGibbsOperator.java
            • phyloclustering
              • TreeClusteringSharedRoutines.java
              • statistics
                • ClusterLabelsVirusesTreeTrait.java
                • MutationsTreeTrait.java
                • AnnotateMuTreeTrait.java
                • muStatistic.java
                • ActiveIndicatorsStatistic.java
                • AnnotateLocationParameterTreeTrait.java
                • KStatistic.java
                • DriverCountStatistic.java
                • NodeNumberTreeTrait.java
                • CausalMutationsLogger.java
                • DriftedTreeClusterLocationsStatistic.java
                • DriftedMuStatistic.java
                • PathStatistic.java
                • indicatorsStatistic.java
                • ClusterLabelsVirusesStatistic.java
              • misc
                • simulateClusters.java
                • mergeAdjacencyMatrixPlots.java
                • obsolete
                  • ClusterOperator.java
                  • ClusterAlgorithmOperator.java
                  • TreeClusterGibbsOperator.java
                  • AGLikelihoodCluster.java
                  • TreeClusterSequentialSampling.java
                  • serumDriftScalingMuOperator.java
                  • ClusterWalkOperatorParser.java
                  • ClusterViruses.java
                  • AGLikelihoodTreeCluster.java
                  • OrderDouble.java
                  • ClusterComparison.java
                  • TiterImporter.java
                  • ClusterWalkOperator.java
              • operators
                • Mu1ScaleActiveScaledMu1IntactOperator.java
                • Mu2ScaleActiveScaledMu2IntactOperator.java
                • TreeClusterAlgorithmOperator.java
                • serumDriftActiveScaledMu1Operator.java
                • muMeanTranslateInactiveMu1Operator.java
                • ProbGenericSiteGibbsOperator.java
                • serumPrecisionSerumLocOperator.java
                • muPrecisionInactiveMuOperator.java
                • RandomWalkOnActiveMu.java
                • randomWalkSerumDriftAndMu.java
                • ProbSitesGibbsOperator.java
              • TreeClusteringVirusesPrior.java
            • DriftedLocationsStatistic.java
            • AntigenicSplitPrior.java
            • MultidimensionalScalingLikelihood.java
            • DiscreteAntigenicTraitLikelihood.java
            • DriftedTraitsLogger.java
            • CRPClusterRandomWalkOperator.java
            • NPAntigenicLikelihood.java
            • AntigenicLikelihood.java
            • ClusterSplitMergeOperator.java
            • DirichletProcessGibbsOperator.java
            • AntigenicTraitLikelihood.java
            • ContinuousAntigenicTraitLikelihood.java
          • siteratemodel
            • GammaSiteRateModel.java
            • SiteRateModel.java
          • epidemiology
            • LogisticGrowthN0ModelParser.java
            • SIRModel.java
            • SIRepidemicModel.java
            • LogisticGrowthN0Model.java
            • ODEDemographicFunction.java
            • DynamicalForce.java
            • LogisticGrowthN0.java
            • SIRepidemicModelParser.java
            • SIRModelParser.java
            • casetocase
              • PartitionedTreeLoggerParser.java
              • CaseToCaseTreeLikelihood.java
              • CaseToCaseTransmissionLikelihood.java
              • periodpriors
                • IndividualPrior.java
                • OneOverStDevPeriodPriorDistribution.java
                • NormalPeriodPriorDistribution.java
                • AbstractPeriodPriorDistribution.java
                • KnownVarianceNormalPeriodPriorDistribution.java
              • BranchMapModel.java
              • BadPartitionException.java
              • operators
                • TransmissionWilsonBaldingA.java
                • InfectionBranchMovementOperator.java
                • TransmissionSubtreeSlideB.java
                • TransmissionTreeOperator.java
                • TransmissionExchangeOperatorB.java
                • TransmissionSubtreeSlideA.java
                • TransmissionWilsonBaldingB.java
                • TransmissionExchangeOperatorA.java
              • PartitionedTreeLogger.java
              • AbstractOutbreak.java
              • SpatialKernel.java
              • PartitionedTreeModelParser.java
              • WithinCaseCoalescent.java
              • PartitionedTreeModel.java
              • CategoryOutbreak.java
              • AbstractCase.java
            • LambertW.java
            • DynamicalVariable.java
            • DynamicalSystem.java
            • SIRepidemic.java
          • branchratemodel
            • PassageBranchRateModel.java
            • AutoCorrelatedBranchRatesDistribution.java
            • DecayingRateModel.java
            • BranchRateGradientWrtIncrements.java
            • ScaledTreeLengthRateModel.java
            • RandomLocalClockModel.java
            • DiscreteTraitBranchRateModel.java
            • AttributeBranchRateModel.java
            • TipBranchRateModel.java
            • RelaxedDriftModel.java
            • ContinuousTraitBranchRateModel.java
            • StrictClockBranchRates.java
            • LocalClockModel.java
            • shrinkage
              • AutoCorrelatedRatesWithBayesianBridge.java
            • FixedDriftModel.java
            • DefaultBranchRateModel.java
            • LatentStateBranchRateModel.java
            • CountableModelMixtureBranchRates.java
            • RateEpochBranchRateModel.java
            • LocalBranchRates.java
            • ContinuousBranchValueProvider.java
            • ContinuousBranchRates.java
            • CompoundBranchRateModel.java
            • SericolaLatentStateBranchRateModel.java
            • AutoCorrelatedGradientWrtIncrements.java
            • BranchSpecificFixedEffects.java
            • DiscretizedBranchRates.java
            • ContinuousEpochBranchRateModel.java
            • ArbitraryBranchRates.java
            • BranchRateModel.java
            • MixtureModelBranchRates.java
            • AbstractBranchRateModel.java
            • CountableMixtureBranchRates.java
            • CountableBranchCategoryProvider.java
          • speciation
            • BranchingLikelihood.java
            • TaxonRichnessBirthDeathModel.java
            • SpeciationModel.java
            • ModelAveragingSpeciationLikelihood.java
            • BetaSplittingModel.java
            • RandomLocalYuleModel.java
            • UltrametricSpeciationModel.java
            • CalibrationPoints.java
            • MultiSpeciesCoalescent.java
            • SpeciesBindings.java
            • BirthDeathSerialSamplingModel.java
            • BirthDeathGernhard08Model.java
            • SpeciationLikelihood.java
            • SpeciesTreeModel.java
            • SpeciesTreeBMPrior.java
            • YuleModel.java
            • BirthDeathSerialSkylineModel.java
            • MaskableSpeciationModel.java
            • SpeciesTreeSimplePrior.java
            • BranchingModel.java
            • CalibrationLineagesIterator.java
        • math
          • ComplexArray.java
          • FastFourierTransform.java
          • CompoundFunction.java
          • UnivariateMinimum.java
          • EmpiricalBayesPoissonSmoother.java
          • MultivariateMonteCarloIntegral.java
          • LogTricks.java
          • Polynomial.java
          • MFWithGradient.java
          • UnivariateFunction.java
          • MittagLefflerFunction.java
          • GammaFunction.java
          • MultivariateMinimum.java
          • KroneckerOperation.java
          • distributions
            • TransformedMultivariateDistribution.java
            • MultivariateKDEDistribution.java
            • BetaDistribution.java
            • Gumbel2Distribution.java
            • GaussianProcessRandomGenerator.java
            • ChiSquareDistribution.java
            • AbstractLKJDistribution.java
            • TruncatedNormalDistribution.java
            • RandomGenerator.java
            • ReflectedNormalDistribution.java
            • BifractionalDiffusionDensity.java
            • HalfNormalDistribution.java
            • TruncatedDistribution.java
            • DirichletDistribution.java
            • GammaKDEDistribution.java
            • InverseWishartDistribution.java
            • SphericalBetaDistribution.java
            • MultivariateNormalDistribution.java
            • NegativeBinomialDistribution.java
            • UniformDistribution.java
            • LKJCholeskyCorrelationDistribution.java
            • WishartStatistics.java
            • MarginalizedAlphaStableDistribution.java
            • ExponentialDistribution.java
            • PoissonDistribution.java
            • NormalGammaDistribution.java
            • DiscreteUniformDistribution.java
            • LKJCorrelationDistribution.java
            • MultivariateDistribution.java
            • TransformedNormalKDEDistribution.java
            • NormalKDEDistribution.java
            • NormalDistribution.java
            • CompoundGaussianProcess.java
            • MultivariateGammaDistribution.java
            • GeneralizedIntegerGammaDistribution.java
            • LogNormalDistribution.java
            • WishartDistribution.java
            • InverseGaussianDistribution.java
            • HalfTDistribution.java
            • Distribution.java
            • BetaKDEDistribution.java
            • LogTransformedNormalKDEDistribution.java
            • LogitTransformedNormalKDEDistribution.java
            • TDistribution.java
            • LaplaceDistribution.java
            • MultivariatePolyaDistributionLikelihood.java
            • GammaDistribution.java
            • WishartSufficientStatistics.java
            • OffsetPositiveDistribution.java
            • KernelDensityEstimatorDistribution.java
            • InverseGammaDistribution.java
          • AdaptableVector.java
          • matrixAlgebra
            • CholeskyDecomposition.java
            • IllegalDimension.java
            • ejml
              • UnrolledDeterminantFromMinor.java
            • LinearEquations.java
            • WrappedVector.java
            • JacobiTransformation.java
            • ReadableVector.java
            • WritableMatrix.java
            • Matrix.java
            • SymmetricMatrix.java
            • missingData
              • MissingOps.java
              • InversionResult.java
              • PermutationIndices.java
            • WritableVector.java
            • Vector.java
            • NonSymmetricComponents.java
            • RobustEigenDecomposition.java
            • LUPDecomposition.java
            • WrappedMatrix.java
            • LargestEigenvalueFinder.java
            • RobustSingularValueDecomposition.java
            • ReadableMatrix.java
          • BigDecimalUtils.java
          • DifferentialEvolution.java
          • MultivariateFunction.java
          • MinimiserMonitor.java
          • Procrustes.java
          • GeneralisedGaussLaguerreQuadrature.java
          • MonteCarloIntegral.java
          • MultivariateIntegral.java
          • MathUtils.java
          • SparseMatrixExponential.java
          • Binomial.java
          • IntegrableUnivariateFunction.java
          • MersenneTwisterFast.java
          • LineFunction.java
          • RiemannApproximation.java
          • ConjugateDirectionSearch.java
          • ErrorFunction.java
          • Poisson.java
          • BFloat.java
          • interfaces
            • PointSeriesWithErrors.java
            • CurveMouseClickListener.java
            • ManyVariableFunction.java
            • ConjugateWishartStatisticsProvider.java
            • OneVariableFunction.java
            • PointSeries.java
            • ParametrizedOneVariableFunction.java
          • ModifiedBesselFirstKind.java
          • MachineAccuracy.java
          • AdaptableCovariance.java
          • Integral.java
          • iterations
            • BisectionZeroFinder.java
            • FunctionalIterator.java
            • NewtonZeroFinder.java
            • IterativeProcess.java
          • ConjugateGradientSearch.java
          • functionEval
            • GammaFunction.java
            • FunctionDerivative.java
            • PolynomialFunction.java
            • DrMath.java
          • BoundsCheckedFunction.java
          • NumericalDerivative.java
        • evomodelxml
          • CSVExporterParser.java
          • branchmodel
            • BranchAssignmentModelParser.java
            • BranchSpecificSubstitutionParameterBranchModelParser.java
            • ArbitrarySubstitutionParameterBranchModelParser.java
            • ExternalInternalBranchModelParser.java
            • RandomBranchModelParser.java
            • EpochBranchModelParser.java
            • RandomBranchAssignmentModelParser.java
            • BranchSpecificBranchModelParser.java
          • TreeTraceAnalysisParser.java
          • treelikelihood
            • HistoryFilterParser.java
            • BeagleOperationParser.java
            • TreeTraitParserUtilities.java
            • OptimizedBeagleTreeLikelihoodParser.java
            • AncestralStateTreeLikelihoodParser.java
            • TraitLoggerParser.java
            • BeagleTreeLikelihoodParser.java
            • ApproximatePoissonTreeLikelihoodParser.java
            • BalancedBeagleTreeLikelihoodParser.java
            • StratifiedTraitLoggerParser.java
            • CompleteHistoryLoggerParser.java
            • MarkovJumpsLikelihoodLoggerParser.java
            • MarkovJumpsTreeLikelihoodParser.java
            • DnDsLoggerParser.java
            • ALSTreeLikelihoodParser.java
          • tipstatesmodel
            • SequenceErrorModelParser.java
          • treedatalikelihood
            • MultiPartitionDataLikelihoodParser.java
            • ContinuousDataLikelihoodParser.java
            • TreeDataLikelihoodParser.java
          • TreeWorkingPriorParsers.java
          • substmodel
            • GeneralSubstitutionModelParser.java
            • GY94CodonModelParser.java
            • MG94CodonModelParser.java
            • MarkovModulatedSubstitutionModelParser.java
            • OldGLMSubstitutionModelParser.java
            • EmpiricalCodonModelParser.java
            • TN93Parser.java
            • FrequencyModelParser.java
            • GLMSubstitutionModelParser.java
            • PCACodonModelParser.java
            • BinarySubstitutionModelParser.java
            • BinaryCovarionModelParser.java
            • HKYParser.java
            • ComplexSubstitutionModelParser.java
            • MutationDeathModelParser.java
            • MarkovModulatedGY94CodonModelParser.java
            • EmpiricalAminoAcidModelParser.java
            • MarkovModulatedHiddenClassRewardParser.java
            • CodonPartitionedRobustCountingParser.java
            • LewisMkSubstitutionModelParser.java
            • GTRParser.java
          • operators
            • FunkyPriorMixerOperatorParser.java
            • RandomWalkIntegerNodeHeightWeightedOperatorParser.java
            • MicrosatelliteBitFlipOperatorParser.java
            • MicrosatelliteFullAncestryImportanceSamplingOperatorParser.java
            • TreeNodeSlideParser.java
            • RateScaleOperatorParser.java
            • TreeBitMoveOperatorParser.java
            • TreeUniformParser.java
            • NNIParser.java
            • SubtreeSlideOperatorParser.java
            • GibbsSubtreeSwapParser.java
            • SubtreeLeapOperatorParser.java
            • ImportancePruneAndRegraftParser.java
            • TreeBitRandomWalkOperatorParser.java
            • EmpiricalTreeDistributionOperatorParser.java
            • ExchangeOperatorParser.java
            • MicrosatelliteModelSelectOperatorParser.java
            • RateSampleOperatorParser.java
            • ImportanceSubtreeSwapParser.java
            • RateVarianceScaleOperatorParser.java
            • FNPRParser.java
            • MicrosatelliteSingleAncestralStateGibbsOperatorParser.java
            • MoveLinkageGroupParser.java
            • FixedHeightSubtreePruneRegraftOperatorParser.java
            • SubtreeJumpOperatorParser.java
            • MicrosatelliteUpDownOperatorParser.java
            • TipStateSwapOperatorParser.java
            • TipLeapOperatorParser.java
            • ImportanceNarrowExchangeParser.java
            • RandomWalkIntegerSetSizeWeightedOperatorParser.java
            • RateExchangeOperatorParser.java
            • GibbsPruneAndRegraftParser.java
            • WilsonBaldingParser.java
            • PatternWeightIncrementOperatorParser.java
          • continuous
            • DataFromTreeTipsParser.java
            • OrderedLatentLiabilityTransformParser.java
            • LeafTraitExtractorParser.java
            • hmc
              • DiffusionGradientParser.java
              • BranchRateGradientParser.java
              • MeanGradientParser.java
              • GraphicalParameterBoundsParser.java
              • MaximizeWrtParameterParser.java
              • FullyConjugateTreeTipsPotentialDerivativeParser.java
              • NodeHeightTransformParser.java
              • AttenuationGradientParser.java
              • PrecisionGradientParser.java
              • LocationScaleGradientParser.java
              • BranchSubstitutionParameterGradientParser.java
              • TreePrecisionDataProductProviderParser.java
              • NodeHeightGradientParser.java
              • TreePrecisionColumnProviderParser.java
            • GaussianProcessFromTreeParser.java
            • RestrictedPartialsParser.java
            • ElementaryVectorDataModelParser.java
          • coalescent
            • GMRFSkyrideLikelihoodParser.java
            • CoalescentIntervalStatisticParser.java
            • MultiTreeIntervalsParser.java
            • GMRFSkyrideGradientParser.java
            • BayesianSkylineLikelihoodParser.java
            • GMRFIntervalHeightsStatisticParser.java
            • OrnsteinUhlenbeckPriorLikelihoodParser.java
            • OldCoalescentSimulatorParser.java
            • BayesianSkylinePopSizeStatisticParser.java
            • GMRFPopSizeStatisticParser.java
            • demographicmodel
              • EmergingEpidemicModelParser.java
              • ConstantExponentialModelParser.java
              • LogisticGrowthModelParser.java
              • ConstantPopulationModelParser.java
              • ExpansionModelParser.java
              • PiecewisePopulationModelParser.java
              • ExponentialGrowthModelParser.java
              • ExponentialLogisticModelParser.java
              • LinearGrowthModelParser.java
              • PowerLawGrowthModelParser.java
              • MultiEpochExponentialModelParser.java
              • ConstantLogisticModelParser.java
              • ExpConstExpDemographicModelParser.java
              • AsymptoticGrowthModelParser.java
              • CataclysmicDemographicModelParser.java
              • EmpiricalPiecewiseModelParser.java
              • TwoEpochDemographicModelParser.java
              • PeakAndDeclineModelParser.java
              • ScaledPiecewiseModelParser.java
              • ExponentialConstantModelParser.java
              • ExponentialSawtoothModelParser.java
              • ConstExpConstModelParser.java
              • ExponentialExponentialModelParser.java
            • LineageCountStatisticParser.java
            • VariableSkylineLikelihoodParser.java
            • CoalescentTreeIntervalStatisticParser.java
            • TreeIntervalsParser.java
            • operators
              • GMRFSkygridBlockUpdateOperatorParser.java
              • BayesianSkylineGibbsOperatorParser.java
              • SampleNonActiveGibbsOperatorParser.java
              • GMRFSkyrideFixedEffectsGibbsOperatorParser.java
              • GMRFSkyrideBlockUpdateOperatorParser.java
              • GaussianProcessSkytrackBlockUpdateOperatorParser.java
              • GaussianProcessSkytrackTreeOperatorParser.java
            • CoalescentSimulatorParser.java
            • CoalescentLikelihoodParser.java
            • GMRFBivariateCurveAnalysisParser.java
            • BNPRSamplingLikelihoodParser.java
            • PiecewisePopulationSizeModelParser.java
            • EBSPAnalysisParser.java
            • GMRFTestLikelihoodParser.java
            • ConstantPopulationSizeModelParser.java
            • GaussianProcessSkytrackLikelihoodParser.java
            • VariableDemographicModelParser.java
            • BMPriorLikelihoodParser.java
            • PopulationSizeGraphParser.java
            • CoalescentEventsStatisticParser.java
            • ExponentialPopulationSizeModelParser.java
            • GPSkytrackAnalysisParser.java
          • tree
            • TreeMetricStatisticParser.java
            • TreeLengthStatisticParser.java
            • AncestralTraitTreeModelParser.java
            • HiddenLinkageModelParser.java
            • TreeLoggerParser.java
            • RLTVLoggerOnTreeParser.java
            • TMRCAStatisticParser.java
            • MRCATraitStatisticParser.java
            • TipHeightLikelihoodParser.java
            • ParsimonyStatisticParser.java
            • HiddenLinkageLoggerParser.java
            • TransformedTreeModelParser.java
            • ParsimonyStateStatisticParser.java
            • UniformNodeHeightPriorParser.java
            • CompatibilityStatisticParser.java
            • TreeModelParser.java
            • ExternalLengthStatisticParser.java
            • SpeciesTreeStatisticParser.java
            • NodeHeightsStatisticParser.java
            • AncestralTraitParser.java
            • TreeShapeStatisticParser.java
            • TreeHeightStatisticParser.java
            • TerminalBranchStatisticParser.java
            • HiddenLinkageTreeLoggerParser.java
            • RateCovarianceStatisticParser.java
            • MicrosatelliteSamplerTreeModelParser.java
            • RateStatisticParser.java
            • TransformedTreeTraitParser.java
            • StarTreeModelParser.java
            • CTMCScalePriorParser.java
            • MonophylyStatisticParser.java
            • EmpiricalTreeDistributionModelParser.java
          • ConditionalCladeFrequencyParser.java
          • siteratemodel
            • GammaSiteModelParser.java
          • branchratemodel
            • LocalBranchRatesParser.java
            • LocalClockModelParser.java
            • FixedDriftModelParser.java
            • RandomLocalClockModelParser.java
            • BranchRateTransformParser.java
            • AttributeBranchRateModelParser.java
            • ScaledTreeLengthRateModelParser.java
            • MixtureModelBranchRatesParser.java
            • BranchCategoriesParser.java
            • CountableMixtureBranchRatesParser.java
            • BranchSpecificFixedEffectsParser.java
            • DiscreteTraitBranchRateModelParser.java
            • DiscretizedBranchRatesParser.java
            • ContinuousTraitBranchRateModelParser.java
            • BranchRateGradientWrtIncrementsParser.java
            • LatentStateBranchRateModelParser.java
            • StrictClockBranchRatesParser.java
            • AutoCorrelatedGradientWrtIncrementsParser.java
            • BranchParameterParser.java
            • ContinuousBranchRatesParser.java
            • AutoCorrelatedRatesBayesianBridgeParser.java
            • ArbitraryBranchRatesParser.java
            • RelaxedDriftModelParser.java
            • RateEpochBranchRateModelParser.java
            • CompoundBranchRateModelParser.java
            • AutoCorrelatedBranchRatesDistributionParser.java
          • WanderingTaxonLoggerParser.java
          • speciation
            • BirthDeathModelParser.java
            • BetaSplittingModelParser.java
            • SpeciesBindingsParser.java
            • MultiSpeciesCoalescentParser.java
            • SpeciesTreeSimplePriorParser.java
            • RLTVLoggerParser.java
            • BirthDeathSerialSkylineModelParser.java
            • BranchingLikelihoodParser.java
            • ModelAveragingSpeciationLikelihoodParser.java
            • SpeciesBindingsSPinfoParser.java
            • BirthDeathSerialSamplingModelParser.java
            • RandomLocalYuleModelParser.java
            • SpeciesTreeBMPriorParser.java
            • YuleModelParser.java
            • BirthDeathEpidemiologyModelParser.java
            • SpeciesTreeModelParser.java
            • SpeciationLikelihoodParser.java
            • TaxonRichnessBirthDeathModelParser.java
        • oldevomodel
          • approxPopTree
            • AbstractPopulationMRCAModel.java
            • CoalescentPopulationMRCAModel.java
            • UniformPopulationMRCAModel.java
            • ConstantPopulationMRCAModel.java
            • PopTreeModel.java
          • lineage
            • LineageModelLikelihood.java
            • LineageSitePatternsParser.java
            • LineageSitePatterns.java
          • treelikelihood
            • EpochTreeLikelihood.java
            • NativeGeneralLikelihoodCore.java
            • AbstractTreeLikelihood.java
            • AbstractLikelihoodCore.java
            • NucleotideLikelihoodCore.java
            • TreeLikelihood.java
            • PurifyingGammaTreeLikelihood.java
            • TreeBranchSubstitutionModel.java
            • PrecisionTestTreeLikelihood.java
            • ScaleFactorsHelper.java
            • ArbitraryPrecisionLikelihoodCore.java
            • MicrosatelliteSamplerTreeLikelihood.java
            • AncestralStateTreeLikelihood.java
            • LikelihoodCore.java
            • NativeNucleotideLikelihoodCore.java
            • EpochTreeBranchSubstitutionModel.java
            • HiddenLinkageLikelihood.java
            • AminoAcidLikelihoodCore.java
            • NodePosteriorTreeLikelihood.java
            • NativeAminoAcidLikelihoodCore.java
            • PurifyingTreeLikelihood.java
            • GeneralLikelihoodCore.java
            • NativeCovarionLikelihoodCore.java
            • AdvancedTreeLikelihood.java
          • ibd
            • HKYRates.java
            • AvgPosteriorIBDReporter.java
            • IBDReporter.java
          • MSSD
            • ALSTreeLikelihood.java
            • AnyTipObservationProcess.java
            • AbstractObservationProcess.java
            • ExponentialBranchLengthTreePrior.java
            • SingleTipObservationProcess.java
          • substmodel
            • PCARateMatrixMammalia.java
            • AbstractCodonModel.java
            • GTR.java
            • GeneralSubstitutionModel.java
            • LG.java
            • CovarionGTR.java
            • MarginalVarianceStatistic.java
            • JTT.java
            • Blosum62.java
            • AbstractAminoAcidModel.java
            • AbstractCovarionModel.java
            • NtdBMA.java
            • ComplexSubstitutionModel.java
            • TwoPhaseModel.java
            • CovarionFrequencyModel.java
            • MutationDeathModel.java
            • MicrosatelliteModel.java
            • AbstractCovarionDNAModel.java
            • MTREV.java
            • FrequencyModel.java
            • TN93.java
            • WAG.java
            • LinearBiasModel.java
            • AminoAcidModelType.java
            • SubstitutionModelUtils.java
            • NucModelType.java
            • SVSGeneralSubstitutionModel.java
            • YangCodonModel.java
            • PseudoCodonModel.java
            • FLU.java
            • EmpiricalRateMatrix.java
            • PCACodonModel.java
            • CPREV.java
            • NewMicrosatelliteModel.java
            • EmpiricalAminoAcidModel.java
            • GeneralF81Model.java
            • SubstitutionEpochModel.java
            • AbstractSubstitutionModel.java
            • AbstractNucleotideModel.java
            • MsatBMA.java
            • OnePhaseModel.java
            • Dayhoff.java
            • EmpiricalCodonRateMatrix.java
            • CovarionHKY.java
            • SVSComplexSubstitutionModel.java
            • AbstractPCARateMatrix.java
            • EmpiricalCodonModel.java
            • BinaryCovarionModel.java
            • TwoStateCovarionModel.java
            • GLMSubstitutionModel.java
            • HKY.java
            • AsymmetricQuadraticModel.java
            • SubstitutionModel.java
            • PositiveDefiniteSubstitutionModel.java
          • clock
            • ACLikelihood.java
            • UniversalClock.java
            • UCLikelihood.java
            • RateEvolutionLikelihood.java
          • indel
            • IstvanOperator.java
            • TKF91Model.java
            • IndelModel.java
            • TKF91Likelihood.java
            • IstvansProposal.java
            • HomologyRecursion.java
            • NativeTreeLikelihood.java
            • IntMathVec.java
          • sitemodel
            • DiscretizedLociRates.java
            • SampleStateModel.java
            • ScoreMatrix.java
            • AlignmentScore.java
            • GammaSiteBMA.java
            • CategorySampleModel.java
            • SiteRateModel.java
            • PairDistance.java
            • SampleQuantileLociRates.java
            • DirichletSiteModel.java
            • SampleStateAndCategoryModel.java
            • CategorySiteModel.java
            • CategoryParameterStatistic.java
            • GammaSiteModel.java
            • SiteModel.java
        • stats
          • DiscreteStatistics.java
          • Regression.java
          • Variate.java
          • FrequencyCounter.java
        • matrix
          • MutableMatrix.java
          • ConcreteMatrix.java
          • Matrix.java
        • inference
          • smc
            • SMCOptions.java
            • SMC.java
          • ml
            • HillClimbingCriterion.java
            • GreatDelugeCriterion.java
            • MLOptimizer.java
          • markovchain
            • MarkovChainListener.java
            • Profiler.java
            • Acceptor.java
            • MarkovChain.java
          • state
            • StateLoader.java
            • StateSaverChainListener.java
            • StateLoaderSaver.java
            • Factory.java
            • StateSaver.java
          • tutorial
            • Tutorial1.java
          • multidimensionalscaling
            • MassivelyParallelMDSImpl.java
            • MultiDimensionalScalingCore.java
            • MultiDimensionalScalingLikelihood.java
            • MultiDimensionalScalingCoreImpl.java
            • NativeMDSSingleton.java
            • mm
              • MultiDimensionalScalingMM.java
              • MMAlgorithm.java
          • mcmc
            • MarginalLikelihoodEstimator.java
            • MCMCCriterion.java
            • MCMCOptions.java
            • MCMC.java
          • trace
            • TraceException.java
            • TraceList.java
            • Filter.java
            • TraceTypeUtils.java
            • TracesListener.java
            • Trace.java
            • TraceCorrelation.java
            • MarginalLikelihoodAnalysis.java
            • PathSamplingAnalysis.java
            • NumberUtils.java
            • TracesReader.java
            • TraceType.java
            • GeneralizedSteppingStoneSamplingAnalysis.java
            • FilteredTraceList.java
            • SteppingStoneSamplingAnalysis.java
            • LogFileTraces.java
            • KernelDensityEstimate.java
            • TraceAnalysis.java
            • TraceDistribution.java
            • DensityRectangle.java
            • DensityEstimate.java
            • AbstractTraceList.java
            • ArrayTraceList.java
            • LogFileTraceExporter.java
          • loggers
            • TabDelimitedFormatter.java
            • Columns.java
            • MatrixEntryColumn.java
            • Loggable.java
            • MLLogger.java
            • LogFormatter.java
            • LogColumn.java
            • ArrayLogFormatter.java
            • PercentColumn.java
            • MCLogger.java
            • Logger.java
            • BooleanColumn.java
            • NumberColumn.java
          • operators
            • ModeFindOperator.java
            • IBPBitFlipOperator.java
            • NegationOperator.java
            • MultivariateNormalGibbsOperator.java
            • GibbsIndependentNormalDistributionOperator.java
            • MaskMoveOperator.java
            • OperatorUtils.java
            • SwapOperator.java
            • RegressionGibbsPrecisionOperator.java
            • SimpleOperator.java
            • OperatorSchedule.java
            • GibbsIndependentJointNormalGammaOperator.java
            • GibbsOperator.java
            • SwapParameterOperator.java
            • repeatedMeasures
              • GammaGibbsProvider.java
            • RandomWalkGammaPrecisionGibbsOperator.java
            • MultivariateNormalIndependenceSampler.java
            • UniformIntegerOperator.java
            • AlternatingOperatorSchedule.java
            • MaximizerWrtParameterOperator.java
            • AdaptationMode.java
            • TreeMaximizationOperator.java
            • RandomWalkOperator.java
            • UpDownOperator.java
            • MultipleRandomWalkIntegerOperator.java
            • EllipticalSliceOperator.java
            • SimpleMCMCOperator.java
            • OperatorAnalysisPrinter.java
            • TeamOperator.java
            • SliceOperator.java
            • TransformedParameterRandomWalkOperator.java
            • SwapParameterGibbsOperator.java
            • shrinkage
              • ShrinkageAugmentedGibbsOperator.java
              • ShrinkageGibbsOperator.java
              • BayesianBridgeShrinkageOperator.java
            • SelectorOperator.java
            • IndependentGammaSampler.java
            • PathDependent.java
            • ValuesPoolSwapOperator.java
            • BitFlipOperator.java
            • hmc
              • BouncyParticleOperator.java
              • deprecated
                • AbstractHamiltonianMCOperator.java
                • LatentFactorHamiltonianMCParser.java
                • LoadingsHamiltonianMC.java
                • LoadingsHamiltonianMCParser.java
                • LatentFactorHamiltonianMC.java
              • AbstractParticleOperator.java
              • NumericalHessianFromGradient.java
              • ZigZagOperator.java
              • ReflectiveHamiltonianMonteCarloOperator.java
              • HamiltonianMonteCarloOperator.java
              • MassPreconditioner.java
              • StepSize.java
              • SecantHessian.java
              • NoUTurnOperator.java
            • IndependentEvaluationOperator.java
            • TwoPhaseOperator.java
            • MVOUCovarianceOperator.java
            • CombinedOperatorSchedule.java
            • GaussianProcessDrawOperator.java
            • TransformedRandomWalkOperator.java
            • AdaptableVarianceMultivariateNormalOperator.java
            • DeltaMixOperator.java
            • ScaleOperator.java
            • RandomWalkIntegerOperator.java
            • DirtyLikelihoodOperator.java
            • JointGibbsOperator.java
            • CenteredScaleOperator.java
            • BitMoveOperator.java
            • MCMCOperator.java
            • MultivariateNormalOperator.java
            • GeneralOperator.java
            • AdaptableMCMCOperator.java
            • SimpleMetropolizedGibbsOperator.java
            • GenericIndependentSampler.java
            • SliceInterval.java
            • BitSwapOperator.java
            • InvariantOperator.java
            • factorAnalysis
              • LoadingsGibbsTruncatedOperator.java
              • FactorRJMCMCOperator.java
              • FactorOperator.java
              • LoadingsRotationOperator.java
              • LatentFactorModelPrecisionGibbsOperator.java
              • LFMTargetedSearchOperator.java
              • FactorAnalysisOperatorAdaptor.java
              • FactorGibbsOperator.java
              • FactorTreeGibbsOperator.java
              • LFMSplitMergeOperator.java
              • LatentFactorLiabilityGibbsOperator.java
              • LoadingsSparsityOperator.java
              • FactorIndependenceOperator.java
              • NewLoadingsGibbsOperator.java
              • LoadingsGibbsOperator.java
              • LoadingsIndependenceOperator.java
            • HierarchicalBitFlipOperator.java
            • AbstractAdaptableOperator.java
            • RegressionGibbsEffectOperator.java
            • RegressionMetropolizedIndicatorOperator.java
            • ModeIndependenceOperator.java
            • DeltaExchangeOperator.java
            • UniformOperator.java
            • FireParameterOperator.java
            • JointOperator.java
            • NormalGammaPrecisionGibbsOperator.java
            • Scalable.java
            • SimpleOperatorSchedule.java
            • RateBitExchangeOperator.java
            • IndependentNormalDistributionSampler.java
            • GibbsIndependentGammaOperator.java
            • NormalNormalMeanGibbsOperator.java
            • SetOperator.java
          • hmc
            • CompoundDerivative.java
            • PrecisionMatrixVectorProductProvider.java
            • DerivativeWrtParameterProvider.java
            • CompoundGradient.java
            • HessianWrtParameterProvider.java
            • MaskedGradient.java
            • LFMFactorPotentialDerivative.java
            • PathGradient.java
            • GradientWrtParameterProvider.java
            • LFMLoadingsPotentialDerivative.java
            • PrecisionColumnProvider.java
            • NormalPotentialDerivative.java
            • SumDerivative.java
          • glm
            • GeneralizedLinearModel.java
          • distribution
            • ExponentialDistributionModel.java
            • ModelSpecificPseudoPriorLikelihood.java
            • LocationScaleJeffreysPrior.java
            • IndependentInverseGammaDistributionModel.java
            • GeneralizedLinearModel.java
            • LinearRegression.java
            • TDistributionModel.java
            • DeterminentalPointProcessPrior.java
            • MarginalizedAlphaStableDistributionModel.java
            • GammaDistributionModel.java
            • TruncatedNormalDistributionModel.java
            • ParametricMultivariateDistributionModel.java
            • BetaDistributionModel.java
            • TwoPartsDistributionLikelihood.java
            • MixedDistributionLikelihood.java
            • SplineInterpolatedLikelihood.java
            • ParametricDistributionModel.java
            • EmpiricalDistributionLikelihood.java
            • DistributionLikelihood.java
            • WishartGammalDistributionModel.java
            • RandomWalkGenerator.java
            • InverseGammaDistributionModel.java
            • DensityModel.java
            • HierarchicalGraphLikelihood.java
            • CauchyDistribution.java
            • ExponentialTiltedStableDistribution.java
            • UniformDistributionModel.java
            • LogLinearModel.java
            • MultivariateDistributionLikelihood.java
            • shrinkage
              • OldMarginalBayesianBridge.java
              • BayesianBridgeDistributionModel.java
              • BayesianBridgeLikelihood.java
              • BayesianBridgeStatisticsProvider.java
              • JointBayesianBridgeDistributionModel.java
              • OldBayesianBridgeLikelihood.java
              • MarginalBayesianBridgeDistributionModel.java
              • OldJointBayesianBridge.java
            • PoissonDistributionModel.java
            • RandomWalkModel.java
            • IndependentNormalDistributionModel.java
            • RowDimensionMultinomialPrior.java
            • LogNormalDistributionModel.java
            • BinomialLikelihood.java
            • NormalDistributionModel.java
            • SkewNormalDistributionModel.java
            • RowDimensionPoissonPrior.java
            • LatentFactorModelInterface.java
            • DirichletProcessLikelihood.java
            • MomentDistributionModel.java
            • LogisticRegression.java
            • CachedDistributionLikelihood.java
            • InverseGaussianDistributionModel.java
            • AbstractDistributionLikelihood.java
            • NegativeBinomialDistributionModel.java
            • MultivariateNormalDistributionModel.java
            • ExponentialMarkovModel.java
            • TwoPieceLocationScaleDistributionModel.java
          • parallel
            • MPILikelihoodRunner.java
            • MPIServices.java
            • MPISerializable.java
            • ServiceRequest.java
          • regression
            • RegressionJNIWrapper.java
            • SelfControlledCaseSeries.java
          • markovjumps
            • MarkovJumpsCore.java
            • MarkovJumpsType.java
            • UniformizedStateHistory.java
            • SubordinatedProcess.java
            • StateHistory.java
            • MarkovReward.java
            • StateChange.java
            • TwoStateOccupancyMarkovReward.java
            • SericolaSeriesMarkovReward.java
            • MarkovJumpsRegisterAcceptor.java
            • TwoStateSericolaSeriesMarkovReward.java
          • model
            • StatisticParser.java
            • RPNexpressionCalculator.java
            • CompoundEigenMatrix.java
            • CorrelationSymmetricMatrix.java
            • MatrixParameter.java
            • Model.java
            • FastTransposedBlockUpperTriangularMatrixParameter.java
            • DummyLikelihood.java
            • GraphicalParameterBound.java
            • CachedMatrixInverse.java
            • ValuesPool.java
            • MeanStatistic.java
            • FastBlockUpperTriangularMatrixParameter.java
            • RPNcalculatorStatistic.java
            • AbstractModelLikelihood.java
            • DerivativeProvider.java
            • OneOnX3Prior.java
            • EqualityConstrainedParameter.java
            • DecomposedMatrix.java
            • MatrixVectorProductParameter.java
            • ProductParameter.java
            • NewMatrixParameter.java
            • LogarithmStatistic.java
            • IntersectionBounds.java
            • CorrelationMatrixStatistic.java
            • BlockDiagonalMatrixParameter.java
            • ExponentialStatistic.java
            • DiagonalCorrelationMatrix.java
            • BooleanStatistic.java
            • Bounds.java
            • DifferenceMatrixParameter.java
            • VarianceProportionStatistic.java
            • DifferenceStatistic.java
            • Parameter.java
            • MaskedParameter.java
            • ValuesPoolParser.java
            • ParameterChooser.java
            • ExpressionStatistic.java
            • TruncatedDistributionLikelihood.java
            • Profileable.java
            • AbstractAlgebraStatistic.java
            • Variable.java
            • AdaptableSizeFastMatrixParameter.java
            • AbstractModel.java
            • TransformedParameter.java
            • LikelihoodBenchmarker.java
            • Statistic.java
            • TraitValidationProvider.java
            • EigenVectorsMatrix.java
            • ParallelLikelihood.java
            • DefaultModel.java
            • BlockUpperTriangularMatrixParameter.java
            • NotBooleanStatistic.java
            • ThresholdStatistic.java
            • RatioStatistic.java
            • CoulombPrior.java
            • Likelihood.java
            • DerivativeOrder.java
            • MatrixInverseStatistic.java
            • ComplementParameter.java
            • FiniteSetParameter.java
            • MatrixParameterInterface.java
            • SplineBasis.java
            • ParameterChooserParser.java
            • DifferenceParameter.java
            • CompoundParameter.java
            • LikelihoodProfile.java
            • VectorSliceParameter.java
            • SumParameter.java
            • OriginDestinationDesignMatrix.java
            • ParameterParser.java
            • TransposedBlockUpperTriangularMatrixParameter.java
            • LikelihoodWithGradient.java
            • MatrixSizePrior.java
            • MarkovRandomFieldMatrix.java
            • OneOnXPrior.java
            • JointParameter.java
            • LoggableStatistic.java
            • ReciprocalStatistic.java
            • PathLikelihood.java
            • DiagonalConstrainedMatrixView.java
            • TestStatistic.java
            • LogOrderedMatrix.java
            • ThreadAwareLikelihood.java
            • IndianBuffetProcessPrior.java
            • ModelListener.java
            • MatrixMatrixProduct.java
            • FastMatrixParameter.java
            • CompoundFastMatrixParameter.java
            • DiagonalMatrix.java
            • WeightedMixtureModel.java
            • CompoundMatrixParameter.java
            • FastCompoundMatrixParameter.java
            • TransformedMultivariateParameter.java
            • ParallelCompoundLikelihood.java
            • BooleanLikelihood.java
            • PearsonCorrelation.java
            • CrossValidationProvider.java
            • CopyParameterValuesParser.java
            • CompoundSymmetricMatrix.java
            • VarianceStatistic.java
            • CompoundLikelihood.java
            • BayesianStochasticSearchVariableSelection.java
            • TransposedMatrixParameter.java
            • MonotonicStatistic.java
            • GradientProvider.java
            • ElementWiseMatrixMultiplicationParameter.java
            • HessianProvider.java
            • BranchParameter.java
            • DuplicatedParameter.java
            • SumStatistic.java
            • AbstractTransformedCompoundMatrix.java
            • EqualityConstraintModel.java
            • LatentFactorModel.java
            • ConstantLikelihood.java
            • TestThreadedCompoundLikelihood.java
            • NegativeStatistic.java
            • VariableListener.java
            • DesignMatrix.java
            • MixtureModelLikelihood.java
            • SubStatistic.java
            • CorrelationStatistic.java
            • CompoundModel.java
            • ProductStatistic.java
            • MatrixValidationProvider.java
            • ThreadedCompoundLikelihood.java
            • NotStatistic.java
            • ParameterIntegerParser.java
            • StatisticList.java
          • mcmcmc
            • MCMCMC.java
            • MCMCMCOptions.java
            • MCMCMCRunner.java
        • app
          • realtime
            • DistanceMatrixInsertionTest.java
            • CheckPointTreeModifier.java
            • CheckPointUpdaterApp.java
            • CheckPointModifier.java
            • SimpleDistanceMatrix.java
          • tempest
            • images
            • TempestMacFileMenuFactory.java
            • TempestDefaultFileMenuFactory.java
            • TempestFrame.java
            • TemporalRooting.java
            • TemporalStress.java
            • TempEstApp.java
            • SamplesPanel.java
            • ParentPlot.java
            • TempestMenuBarFactory.java
            • TempestPanel.java
            • TreeUtils.java
            • RootToTip.java
          • plugin
            • Plugin.java
            • PluginLoader.java
          • phylogeography
            • tools
              • TreeGeoJSONGenerator.java
              • DiscreteTreeToKML.java
              • TreeDensityKML.java
              • ContinuousTreeToKML.java
              • DiscreteKMLString.java
              • RateIndicatorBF.java
              • AuspiceGenerator.java
              • kml
                • BranchStyle.java
                • TreeDefinition.java
                • AnalysisType.java
                • LineStyle.java
                • Location.java
                • TreeSettings.java
                • SurfaceDecoration.java
                • Settings.java
                • TreeType.java
              • ContinuousKML.java
              • DiscreteRatePriorGenerator.java
              • TreeKMLGenerator.java
          • bss
            • PartitionTableModel.java
            • DefaultEditMenuFactory.java
            • RootSequenceEditor.java
            • icons
            • TaxaEditor.java
            • FileMenuHandler.java
            • FrequencyModelEditor.java
            • AnalysisException.java
            • BeagleSequenceSimulatorConsoleApp.java
            • RowNumberTable.java
            • TerminalPanel.java
            • SimulationPanel.java
            • PartitionDataList.java
            • BranchSubstitutionModelEditor.java
            • TaxaEditorTableModel.java
            • ClockRateModelEditor.java
            • XMLExporter.java
            • JTableButtonCellRenderer.java
            • Utils.java
            • ExceptionHandler.java
            • TreesTableRecord.java
            • test
              • BeagleSeqSimTest.java
              • AncestralSequenceTrait.java
            • PartitionData.java
            • TaxaPanel.java
            • JTableComboBoxCellEditor.java
            • JTableComboBoxCellRenderer.java
            • DefaultHelpMenuFactory.java
            • BeagleSequenceSimulatorApp.java
            • SiteRateModelEditor.java
            • JTableButtonCellEditor.java
            • Changelog
            • README.textile
            • DefaultFileMenuFactory.java
            • ColumnResizer.java
            • TaxaTableModel.java
            • PartitionsPanel.java
            • TreesPanel.java
            • TableColumnHider.java
            • AboutDialog.java
            • DemographicModelEditor.java
            • SimpleFileFilter.java
            • TreesTableModel.java
            • DisabledItemsComboBox.java
            • MenuBarFactory.java
            • MainFrame.java
            • XMLGenerator.java
            • JTableButtonMouseListener.java
          • seqgen
            • RecomboGen.java
            • MicrosatelliteSimulator.java
            • GeoDiffusionSimulator.java
            • SeqGen.java
            • SequenceSimulator.java
          • pathogen
            • PathogenFrame.java
            • images
            • PathogenMacFileMenuFactory.java
            • PathogenApp.java
            • PathogenPanel.java
            • TemporalRooting.java
            • PathogenDefaultFileMenuFactory.java
            • PathogenMenuBarFactory.java
            • TemporalStress.java
            • SamplesPanel.java
            • ParentPlot.java
            • TreeUtils.java
            • RootToTip.java
          • util
            • OSType.java
            • Arguments.java
            • Utils.java
          • treespace
            • inputpanel
              • InputFileSettingsDialog.java
              • InputPanel.java
            • MacFileMenuFactory.java
            • TreeSpaceApp.java
            • images
            • TreePlotter.java
            • CladeSystem.java
            • CladePlotter.java
            • InputFile.java
            • TreeSpaceDocument.java
            • TreeSpaceMenuBarFactory.java
            • TreePanel.java
            • TreeSpaceFrame.java
            • renderpanel
              • RenderPanel.java
            • TreeLineages.java
            • CladePanel.java
          • vcs
            • VariableCoalescentSimulator.java
            • VCS.tex
          • gui
            • SelectAllActionResponder.java
            • DeleteActionResponder.java
            • components
              • ColorWellButton.java
              • RealNumberField.java
              • WholeNumberField.java
              • JVerticalLabel.java
            • table
              • TableEditorStopper.java
              • TaxonListTable.java
              • TableSorter.java
              • images
              • MultiLineTableCellContent.java
              • DateCellEditor.java
              • WholeNumberCellEditor.java
              • MultiLineTableCellRenderer.java
              • RealNumberCellEditor.java
            • util
              • LongTaskMonitor.java
              • TaskListener.java
              • CorrelationData.java
              • LongTask.java
              • SimpleLongTask.java
              • SwingWorker.java
            • ColorFunction.java
            • chart
              • JChart.java
              • AreaPlot.java
              • ViolinPlot.java
              • ChartException.java
              • ChartSetupDialog.java
              • ColumnPlot.java
              • IntegerViolinPlot.java
              • JChartPanel.java
              • ErrorBarPlot.java
              • DiscreteAxis.java
              • LineDistributionPlot.java
              • PDFPlot.java
              • KDESetupDialog.java
              • ChartSelector.java
              • HistogramPlot.java
              • JGridChart.java
              • XY.java
              • LinePlot.java
              • TangHuLuPlot.java
              • LinearAxis.java
              • NumericalDensityPlot.java
              • CorrelationPlot.java
              • ChartRuntimeException.java
              • BoxPlot.java
              • JParallelChart.java
              • RegressionPlot.java
              • Axis.java
              • LogAxis.java
              • ChartLayout.java
              • Plot.java
              • KDENumericalDensityPlot.java
              • ScatterPlot.java
              • BlankAxis.java
              • CustomAxis.java
            • FileDrop.java
            • tree
              • SquareTreePainter.java
              • JTreeDisplay.java
              • JTreePanel.java
              • NodeDecorator.java
              • NodeHeightBoxPlot.java
              • CoordinateTransform.java
              • TreePainter.java
          • misc
            • Coevolve.java
          • coalgen
            • InputsPanel.java
            • images
            • DataPanel.java
            • CoalGenApp.java
            • SimulationsPanel.java
            • CoalGenMenuFactory.java
            • CoalGenFrame.java
            • ModelPanel.java
            • CoalGenData.java
          • checkpoint
            • DebugTreeImporter.java
            • BeastCheckpointer.java
            • checkpointing.md
          • beagle
            • tools
              • parsers
                • BeagleSequenceSimulatorParser.java
                • PartitionParser.java
                • CompleteHistorySimulatorParser.java
                • SiteLogLikelihoodLoggerParser.java
              • SiteLogLikelihoodLogger.java
              • Partition.java
              • CompleteHistorySimulator.java
              • BeagleSequenceSimulator.java
          • beastgen
            • NexusApplicationImporter.java
            • BEASTGen.java
            • BeastImporter.java
            • DataModelImporter.java
          • bfe
            • XMLMerger.java
            • BFEapp.form
            • XMLViewer.form
            • BFEapp.java
            • XMLTreeModel.java
            • XMLMerger.form
            • XMLViewer.java
            • BFEMain.java
          • treestat
            • StatisticsPanel.java
            • statistics
              • CladeMeanAttributeStatistic.java
              • TreeLength.java
              • RootToTipLengths.java
              • GammaStatistic.java
              • Nbar.java
              • SingleChildCountStatistic.java
              • TMRCASummaryStatistic.java
              • ExternalBranchRates.java
              • IntervalKStatistic.java
              • RankProportionStatistic.java
              • TreeHeight.java
              • CherryStatistic.java
              • AbstractTreeSummaryStatistic.java
              • DeltaStatistic.java
              • SummaryStatisticDescription.java
              • LineageProportionStatistic.java
              • InternalBranchLengths.java
              • MRCAOlderThanStatistic.java
              • LineageCountStatistic.java
              • FuLiD.java
              • TreenessStatistic.java
              • ExternalInternalRatio.java
              • TreeSummaryStatistic.java
              • CollessIndex.java
              • InternalNodeAttribute.java
              • NodeHeights.java
              • InternalBranchRates.java
              • B1Statistic.java
              • CladeMRCAAttributeStatistic.java
              • BetaTreeDiversityStatistic.java
            • TableSorter.java
            • images
            • TreeStatPanel.java
            • TreeStatData.java
            • CharactersPanel.java
            • TreeStatApp.java
            • TreeStatFrame.java
            • TaxonSetsPanel.java
          • beauti
            • BeautiApp.java
            • options
              • ModelOptions.java
              • AbstractPartitionData.java
              • GlobalModelOptions.java
              • MicrosatelliteOptions.java
              • PartitionOptions.java
              • PartitionTreePrior.java
              • TreeModelOptions.java
              • Parameter.java
              • ComponentOptions.java
              • PartitionData.java
              • TraitData.java
              • PartitionTreeModel.java
              • GuessDatesException.java
              • DateGuesser.java
              • ClockModelOptions.java
              • Operator.java
              • PartitionSubstitutionModel.java
              • TraitGuesser.java
              • PartitionPattern.java
              • Predictor.java
              • BeautiOptions.java
              • PartitionClockModel.java
            • priorspanel
              • AbstractPriorDialog.java
              • PriorSettingsPanel.java
              • SpecialNumberPanel.java
              • PriorOptionsPanel.java
              • JointPriorDialog.java
              • DefaultPriorTableDialog.java
              • SelectParametersDialog.java
              • PriorsPanel.java
              • PriorTableModel.java
              • PriorDialog.java
              • HierarchicalPriorDialog.java
            • images
            • alignmentviewer
              • AlignmentViewer.java
              • RowDecorator.java
              • VolumeAminoAcidDecorator.java
              • StateDecorator.java
              • AlignmentBuffer.java
              • HydropathyAminoAcidDecorator.java
              • PlotPane.java
              • ChemicalAminoAcidDecorator.java
              • AminoAcidDecorator.java
              • AlignmentBufferListener.java
              • TaxonPane.java
              • AlignmentPane.java
              • RulerPane.java
              • StateCellDecorator.java
              • NucleotideDecorator.java
              • CellDecorator.java
              • ColumnDecorator.java
            • mcmcpanel
              • MCMCPanel.java
            • BeautiFrame.java
            • ComboBoxRenderer.java
            • BeautiMacFileMenuFactory.java
            • tipdatepanel
              • GuessDatesDialog.java
              • SetValueDialog.java
              • TipDatesPanel.java
            • components
              • discrete
                • DiscreteTraitsComponentOptions.java
                • DiscreteTraitsComponentGenerator.java
                • DiscreteSubstModelType.java
                • DiscreteTraitsComponentFactory.java
              • hpm
                • HierarchicalModelComponentGenerator.java
                • HierarchicalModelComponentFactory.java
                • HierarchicalPhylogeneticModel.java
                • HierarchicalModelComponentOptions.java
              • continuous
                • ContinuousSubstModelType.java
                • ContinuousComponentGenerator.java
                • ContinuousComponentOptions.java
                • ContinuousComponentFactory.java
              • ComponentFactory.java
              • ancestralstates
                • AncestralStatesComponentFactory.java
                • AncestralStatesComponentGenerator.java
                • AncestralStatesComponentOptions.java
              • tipdatesampling
                • TipDateSamplingComponentGenerator.java
                • TipDateSamplingComponentOptions.java
                • TipDateSamplingComponentFactory.java
              • dollo
                • DolloComponentOptions.java
                • DolloComponentGenerator.java
                • DolloComponentFactory.java
              • sequenceerror
                • SequenceErrorModelComponentGenerator.java
                • SequenceErrorModelComponentFactory.java
                • SequenceErrorModelComponentOptions.java
              • marginalLikelihoodEstimation
                • MarginalLikelihoodEstimationComponentFactory.java
                • MarginalLikelihoodEstimationOptions.java
                • MLEGSSDialog.java
                • MLEDialog.java
                • MarginalLikelihoodEstimationGenerator.java
              • linkedparameters
                • LinkedParameterComponentGenerator.java
                • LinkedParameterComponentOptions.java
                • LinkedParameterComponentFactory.java
                • LinkedParameter.java
            • util
              • TextUtil.java
              • NexusApplicationImporter.java
              • BEAUTiImporter.java
              • BeastImporter.java
              • NumberUtil.java
              • PartitionNameDialog.java
              • PanelUtils.java
              • XMLWriter.java
              • TreeUtils.java
            • ancestralstatespanel
              • AncestralStatesOptionsPanel.java
              • AncestralStatesPanel.java
            • BeautiPanel.java
            • traitspanel
              • TraitsPanel.java
              • GuessTraitDialog.java
              • GuessTraitException.java
              • CreateTraitDialog.java
              • TraitValueDialog.java
            • BeautiDefaultFileMenuFactory.java
            • types
              • FixRateType.java
              • TreePriorParameterizationType.java
              • TreePriorType.java
              • MicroSatModelType.java
              • TipDateSamplingType.java
              • StartingTreeType.java
              • OperatorSetType.java
              • PriorScaleType.java
              • ClockType.java
              • PriorType.java
              • ParameterFlavour.java
              • HierarchicalModelType.java
              • OperatorType.java
              • SequenceErrorType.java
              • ClockDistributionType.java
              • BinaryModelType.java
              • PopulationSizeModelType.java
              • FrequencyPolicyType.java
            • BeautiMenuBarFactory.java
            • clockmodelspanel
              • PartitionClockModelPanel.java
              • CloneModelDialog.java
              • ClockModelsPanel.java
            • generator
              • OperatorsGenerator.java
              • ParameterPriorGenerator.java
              • TreeLikelihoodGenerator.java
              • AlignmentGenerator.java
              • ClockModelGenerator.java
              • SubstitutionModelGenerator.java
              • TreeModelGenerator.java
              • ComponentGenerator.java
              • PatternListGenerator.java
              • LogGenerator.java
              • TreePriorGenerator.java
              • TMRCAStatisticsGenerator.java
              • Generator.java
              • InitialTreeGenerator.java
              • BaseComponentGenerator.java
              • BeastGenerator.java
            • datapanel
              • SelectTreeDialog.java
              • ViewAligmentPanel.java
              • DataPanel.java
              • SelectModelDialog.java
              • SelectClockDialog.java
              • SelectTraitDialog.java
              • BeautiAlignmentBuffer.java
            • sitemodelspanel
              • PartitionModelPanel.java
              • GLMSettingsDialog.java
              • CloneModelDialog.java
              • GLMSettingsPanel.java
              • SiteModelsPanel.java
            • treespanel
              • PartitionTreeModelPanel.java
              • TreeDisplayPanel.java
              • PartitionTreePriorPanel.java
              • GenerateTreeDialog.java
              • TreesPanel.java
            • operatorspanel
              • OperatorsPanel.java
            • taxonsetspanel
              • TaxonSetPanel.java
          • beast
            • RBeastMain.java
            • images
            • beagle_parsers.properties
            • BeastParser.java
            • BeastRemote.java
            • BeastMain.java
            • release_parsers.properties
            • old_parsers.properties
            • BeastDialog.java
            • development_parsers.properties
            • BeastMPI.java
            • BeastVersion.java
            • beast.properties
          • tools
            • OrderNexusTranslationTable.java
            • TreeAnnotatorDialog.java
            • DensityPlotter.java
            • MixtureModelLogAnalyser.java
            • MakeAncestralSequenceAnnotatedTree.java
            • SpeciesDelimitationAnalyser.java
            • BeastParserDoc.java
            • SkylineReconstructor.java
            • NodeStateAnalyser.java
            • TaxaMarkovJumpHistoryAnalyzer.java
            • BaseTreeTool.java
            • TreeMarkovJumpHistoryAnalyzer.java
            • images
            • TreeAnnotator.java
            • TreeLengthFinder.java
            • TreePruner.java
            • NexusExporter.java
            • AncestralSequenceAnnotator.java
            • GenerateRelaxedClockXMLByData.java
            • Branch2dRateToGrid.java
            • SpliceBeastFiles.java
            • ConvertMigrateTrees.java
            • BranchRatePlotter.java
            • JumpHistoryAnalyser.java
            • TreeSummary.java
            • LogCombinerDialog.java
            • TaxaOriginTrait.java
            • TreeLogAnalyser.java
            • AntigenicPlotter.java
            • GetNSCountsFromTrees.java
            • NormaliseMeanTreeRate.java
            • TopologyTracer.java
            • TransmissionTreeToVirusTree.java
            • LogCombiner.java
            • GetDateFromTree.java
            • DensityMap.java
            • BranchJumpPlotter.java
            • LogAnalyser.java
            • TimeSlicer.java
            • GetAncestralSequenceFromSplitTrait.java
          • mapper
            • application
              • MapperApp.java
              • images
              • StrainsPanel.java
              • MapperDocument.java
              • GeneralPreferencesSection.java
              • MeasurementsPanel.java
              • MapperFrame.java
              • MapperFrameOld.java
              • menus
                • MapperMenuBarFactory.java
                • MapperDefaultFileMenuFactory.java
                • MapperFileMenuHandler.java
                • MapperMacFileMenuFactory.java
              • mapper
                • MapperPanel.java
                • Layer.java
                • Analysis.java
                • LayerType.java
                • AnalysisListener.java
              • LocationsPanel.java
        • evoxml
          • MicrosatellitePatternParser.java
          • UncertainAttributePatternsParser.java
          • RescaledTreeParser.java
          • PolarCoordinatesParser.java
          • NewickParser.java
          • MicrosatelliteSimulatorParser.java
          • SitePatternsParser.java
          • OldHiddenNucleotideParser.java
          • CompositeDataTypeParser.java
          • MicrosatellitePatternStatisticParser.java
          • SimpleNodeParser.java
          • MaskedPatternsParser.java
          • LinkedGroupParser.java
          • MultiLociDistanceParser.java
          • GeneralDataTypeParser.java
          • KStateDataTypeParser.java
          • RandomSubsetTaxaParser.java
          • SequenceParser.java
          • SimpleTreeParser.java
          • NeighborJoiningParser.java
          • util
            • XMLUnits.java
            • DataTypeUtils.java
            • GraphMLUtils.java
            • DateUnitsType.java
          • ConstantPatternsParser.java
          • ConvertAlignmentParser.java
          • LocationParser.java
          • PatternSubSetParser.java
          • TaxaParser.java
          • PearsonCorrelationParser.java
          • MutationDeathTypeParser.java
          • AlignmentParser.java
          • BifractionalDiffusionModelParser.java
          • LineageCountThroughTimeParser.java
          • MetagenomeDataParser.java
          • TaxonParser.java
          • AscertainedSitePatternsParser.java
          • UPGMATreeParser.java
          • LinkageConstraintsParser.java
          • MicrosatelliteParser.java
          • AttributePatternsParser.java
          • MergePatternsParser.java
          • DateParser.java
          • DistanceMatrixParser.java
          • HypermutantAlignmentParser.java
          • RandomTaxaSampleParser.java
    • build_tempest.xml
    • build.xml
    • build_phylogeography.xml
    • build_bss.xml
    • build_coalsim.xml
    • release_phylogeography
      • common
        • lib
        • README.txt
        • bin
          • timeslicer
          • discrete_rate_prior_generator
          • discrete_tree_to_kml
          • continuous_tree_to_kml
          • beastgen
          • rate_indicator_bf
    • examples
      • EmpiricalCodonModels
        • testPCMcodonModel.xml
        • codon-data
          • ecmdata
            • rates_zs.csv
            • freqs_k_unrest.csv
            • freqs_zs.csv
            • inirates.csv
            • norates.csv
            • rates_k_unrest.csv
          • pcadata
            • freqs.csv
            • startfacs.csv
            • means.csv
            • scales.csv
        • testECMcodonModel.xml
      • Benchmarks
        • old_benchmark.xml
      • MDS
        • US_cities.xml
        • US_cities.txt
      • TestXML
        • testML.xml
        • testFactorDrift.xml
        • testPopTreeModel.xml
        • testPreOrderGradients.xml
        • testAddPatterns2.xml
        • testOUDiagonalDiffusion.xml
        • testMCMC.xml
        • testBeastUnitTest.xml
        • testHmcNormalVsLogNormal.xml
        • testStarTreeTest2.xml
        • testMixedModel.xml
        • testLatentLiability.xml
        • testPreOrderGradientsCompare.xml
        • testDiffusionHmcVariance.xml
        • testMissingIntegratedTraitLikelihood.xml
        • testSequenceSimulator.xml
        • testRestrictedAncestralReconstruction.xml
        • testIntegratedFactorModel.xml
        • testMC3.xml
        • testBPOwithMask.xml
        • testMSSD.xml
        • testMVN.xml
        • testTipDatePrecision.xml
        • testInfiniteRootPrecision.xml
        • testAncestralReconstruction.xml
        • testOUDiffusion.xml
        • testJointTipAges.xml
        • testEigenDecompositionMatrix.xml
        • testOUDiffusionHmcPrecision.xml
        • testOUDiffusionHmcAttenuation.xml
        • testFullConditionals.xml
        • testStarTreeTest.xml
        • testLewisMk.xml
        • testDriftDiffusion.xml
        • testGaussianProcessFromTree.xml
        • testDiffusionHmcPrecisionWithNAs.xml
        • testMultiThreading.xml
        • testReflectiveHMC.xml
        • testBPOLatentOnly.xml
        • testSequenceConditionalDistributions.xml
        • testLognormalPrior.xml
        • testCrossValidation.xml
        • testAlignmentStatistics.xml
        • testUncertainSequences.xml
        • testComparativeMethod.xml
        • testCorrelationLKJDistribution.xml
        • testUniformizedMarkovJumps.xml
        • testOUDiagonalDiffusionEstimation.xml
        • testGoudllersSmallprob.xml
        • TreePriors
          • testCoalescent.xml
          • testGMRFCoalescent.xml
          • testBSP1.xml
          • testCoalescentNoClock.xml
          • testCoalescentNoClock1.xml
          • testYuleModel_10taxa.xml
          • testBSPNoClock.xml
          • testExponentialGrowth.xml
          • testCataclysmCoalescent.xml
          • testLinearBSP.xml
          • testYuleOneSite.xml
          • testConstantPopulationSizeModel.xml
          • testConstantSize.xml
          • testBSP.xml
          • testEBSP.xml
          • testBirthDeathModel_10taxa.xml
          • testYuleModel.xml
          • testPiecewiseExponential.xml
          • testExponentialPopulationSizeModel.xml
          • testPiecewisePopulationSizeModel.xml
          • testYuleCase3.xml
          • testYule.xml
        • testPosteriorIBD.xml
        • testMvnHmcCompare.xml
        • testMvnHmc.xml
        • testIOUDiffusion.xml
        • testBPO.xml
        • testGradients.xml
        • testElementaryVectorDataModel.xml
        • testNormalModelGibbs.xml
        • testLikelihood.xml
        • testMVOU.xml
        • testAscertainment.xml
        • testZigZag.xml
        • testBranchGradients.xml
        • testRepeatedMeasures.xml
        • testPathSamplingMultivariateDiffusion.xml
        • testTransmissionStatistic.xml
        • testBinaryDollo.xml
        • testNormalModelEllipticalSliceSampler.xml
        • testSimplePathSampling.xml
        • testRestrictedPartials.xml
        • testTransposedMatrixParameter.xml
        • testJointInternalSample.xml
        • testTreePathSampling.xml
        • testPrecisionWishartLKJDistribution.xml
        • testInjectedMissingness.xml
        • testMvnHmcPreConditioning.xml
        • testMissingTraits.xml
        • testOUCheckPoint.xml
        • testPrimateOUSymmetricPathological6.xml
        • testTreePrecisionColumn.xml
        • testRootMeanUpdate.xml
        • testNewLatentLiabilityGibbs.xml
        • testAutocorrelatedRelaxedClock.xml
        • ClockModels
          • testStrictClockTipDatesSampling.xml
          • testUCRelaxedClockContinuousQuantileLogNormal.xml
          • testUCRelaxedClockLogNormal.xml
          • testStrictClock.xml
          • testUCRelaxedClockGamma.xml
          • testRandomLocalClock.xml
          • testStrictClockTipTime.xml
          • testStrictClockNoDate2.xml
          • testStrictClockNoDate.xml
        • testPMD.xml
        • testTruncatedNormal.xml
        • testCodonLikelihood.xml
        • testReflectiveHMConFixedBounds.xml
        • testTruncatedNormal15dimension.xml
        • SubstModels
          • testSRD06CP12_3.xml
          • testSiteModelAlpha.xml
        • testDiffusionHmcPrecision.xml
        • TreePriors+ClockModels
          • BayesianSkyline+unccorelatedExp.xml
          • GMRFBayesianSkyride+strict .xml
          • constant+uncorrelatedExp.xml
          • extendedBayesianSkyline+uncorrelatedLn.xml
          • birthDeath+unccorelatedLn.xml
          • Yule+unccorelatedExp.xml
          • expansionDoubling+strict.xml.xml
          • exponentialDoubling+strict.xml
        • testMarkovJumps.xml
      • test.sh
      • Recombination
        • arg-ecoli.xml
        • arg-lepto.xml
      • Phylogeography
        • H5N1_HA_discrete.xml
        • continuous