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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