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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