All Classes

  • AbstractAlignment
  • AbstractLeafNode
  • AbstractParentableConstrainedNode
  • AbstractRateMatrix
  • AlgorithmCallback
  • AlgorithmCallback.Utils
  • Alignment
  • AlignmentBuilder
  • AlignmentDistanceMatrix
  • AlignmentGenerator
  • AlignmentGenerator.Utils
  • AlignmentParseException
  • AlignmentReaders
  • AlignmentReaders.PhylipClustalAlignment
  • AlignmentReaders.UnalignedAlignment
  • AlignmentReceiver
  • AlignmentReceiver.BucketReceiver
  • AlignmentReceiver.SingleReceiver
  • AlignmentTool
  • AlignmentUtils
  • AmbiguousDataType
  • AminoAcidModel
  • AminoAcidModelID
  • AminoAcids
  • AnnotationAlignment
  • Assessor
  • Attribute
  • AttributeNode
  • Binomial
  • BLOSUM62
  • BootstrappedAlignment
  • BootstrapStatistics
  • BoundsCheckedFunction
  • BranchAccess
  • BranchAccess.Utils
  • BranchLimits
  • CachedRateMatrix
  • CharacterAlignment
  • ChiSquareDistribution
  • ChiSquareTest
  • ChiSquareValue
  • CircularGraphics
  • CladeSystem
  • ClassDistribution
  • ClockTree
  • ClusterTree
  • ClusterTree.ClusteringMethod
  • CoalescentException
  • CoalescentIntervals
  • CoalescentSimulator
  • CoalescentTree
  • CodonModel
  • Codons
  • CodonTable
  • CodonTableFactory
  • CodonTableUtils
  • Comparable
  • ComparableDouble
  • Comparator
  • ConcatenatedAlignment
  • ConcatenatedAnnotatedAlignment
  • ConditionalProbabilityStore
  • ConditionalProbabilityStore.ExtraProcessor
  • ConjugateDirectionSearch
  • ConjugateGradientSearch
  • ConstantIndependentSingleSplitDistribution
  • ConstantMutationRate
  • ConstantPopulation
  • Constants
  • ConstExpConst
  • ConstExpGrowth
  • ConstrainedInternalNode
  • ConstrainedLeafNode
  • ConstrainedNode
  • ConstrainedNode.HeightAdjustment
  • ConstraintModel
  • ConstraintModel.GroupManager
  • ContigencyTable
  • CPREV
  • DataTranslator
  • DataType
  • DataType.Utils
  • DataTypeTool
  • Dayhoff
  • DefaultCache
  • DeltaModel
  • DeltaModel.Instance
  • DeltaModel.Utils
  • DemographicClockTree
  • DemographicLikelihoodValue
  • DemographicModel
  • DemographicTree
  • DemographicValue
  • DifferentialEvolution
  • DiscreteStatistics
  • DistanceMatrix
  • DistanceMatrixAccess
  • DistanceMatrixAccess.Utils
  • DistanceMatrixGenerator
  • DistanceMatrixGenerator.Utils
  • DistanceMatrixUtils
  • DistanceParseException
  • DistanceTool
  • DoubleKey
  • DoubleKeyCache
  • ElementFactory
  • ElementParser
  • ErrorFunction
  • EvaluationCounter
  • ExpandingPopulation
  • ExponentialDistribution
  • ExponentialGrowth
  • ExternalParameterListener
  • F81
  • F84
  • FastFourStateLHCalculator
  • FastLikelihoodCalculator
  • FisherExact
  • FixedBSRDTGlobalClockModel
  • FixedSRDTGlobalClockModel
  • FormattedInput
  • FormattedOutput
  • FreeBranch
  • FreeInternalNode
  • FreeLeafNode
  • FreeNode
  • GammaDistribution
  • GammaFunction
  • GammaRates
  • GapBalanced
  • GapBalancedAlignment
  • GeneralConstraintGroupManager
  • GeneralConstraintGroupManager.LikelihoodScoreAccess
  • GeneralConstraintGroupManager.Store
  • GeneralConstructionTool
  • GeneralizedDEOptimizer
  • GeneralLikelihoodCalculator
  • GeneralLikelihoodSearcher
  • GeneralObjectState
  • GeneralOptimisable
  • GeneralPoissonRateMatrix
  • GeneralRateDistributionSubstitutionModel
  • GeneralREVRateMatrix
  • GeneralTopologyPool
  • GeneralTreeComponent
  • Genotype
  • GlobalClockModel
  • GroupLeader
  • GTR
  • HeapSort
  • HeightInformationUser
  • HKY
  • Identifier
  • IdGenerator
  • IdGroup
  • IdGroup.Utils
  • IndelAlignment
  • IndelAnnotatedAlignment
  • IndividualParameterHandler
  • IndividualParameterHandler.Listener
  • IndividualParameterHandler.Utils
  • InputSource
  • IntervalsExtractor
  • InvariableSites
  • IUPACNucleotides
  • IUPACPenaltyTable
  • JTT
  • JukesCantorDistanceMatrix
  • JumbledAlignment
  • KishinoHasegawaTest
  • LabelDisplayer
  • LabelDisplayer.Utils
  • LabelMapping
  • LabelMapping.Relabeller
  • LayoutTracker
  • LHCalculator
  • LHCalculator.AbstractExternal
  • LHCalculator.External
  • LHCalculator.Factory
  • LHCalculator.Generator
  • LHCalculator.Internal
  • LHCalculator.Leaf
  • LikelihoodCalculator
  • LikelihoodEvaluator
  • LikelihoodEvaluator.MLResult
  • LikelihoodEvaluator.SimpleMLResult
  • LikelihoodEvaluator.Utils
  • LikelihoodOptimiser
  • LikelihoodRatioTest
  • LikelihoodSummary
  • LikelihoodTool
  • LikelihoodValue
  • LineFunction
  • LinkageDisequilibrium
  • LinkageDisequilibriumComponent
  • LMSSolver
  • LMSSolver.Utils
  • Local
  • Log
  • Logger
  • LogParameterizedTree
  • MachineAccuracy
  • Markable
  • MathUtils
  • Matrix
  • MatrixExponential
  • MersenneTwisterFast
  • MFWithGradient
  • MinimiserMonitor
  • MinimiserMonitor.Utils
  • ModelParameters
  • ModelSupport
  • MolecularClockLikelihoodModel
  • MolecularClockLikelihoodModel.External
  • MolecularClockLikelihoodModel.HeightConverter
  • MolecularClockLikelihoodModel.Instance
  • MolecularClockLikelihoodModel.Internal
  • MolecularClockLikelihoodModel.Leaf
  • MolecularClockLikelihoodModel.Simulator
  • MolecularDataType
  • MolecularDataType.Utils
  • MRDTGlobalClockModel
  • MTREV24
  • MultiLocusAnnotatedAlignment
  • MultiParameterized
  • MultiParameterized.ParameterAccessWatcher
  • MultiRateMatrixHandler
  • MultivariateFunction
  • MultivariateMinimum
  • MultivariateMinimum.Factory
  • MutableDouble
  • MutationRateModel
  • MutationRateModel.Factory
  • MutationRateModelTree
  • Nameable
  • NameColouriser
  • NamedParameterized
  • NeighborJoiningTree
  • NeoParameterized
  • NeoRateMatrix
  • NeutralSelectionRateMatrixGroup
  • NexusParseException
  • NexusTokenizer
  • Node
  • NodeAccess
  • NodeFactory
  • NodeUtils
  • NormalDistribution
  • NucleotideModel
  • NucleotideModelID
  • Nucleotides
  • NumericalDerivative
  • NumericDataType
  • ObjectState
  • OrderEnumerator
  • OrderEnumerator.OEFactory
  • OrderEnumerator.Utils
  • OrthogonalHints
  • OrthogonalHints.Utils
  • OrthogonalLineFunction
  • OrthogonalSearch
  • OrthogonalSearch.RoundOptimiser
  • OutputTarget
  • Painter
  • PairwiseDistance
  • PalEventMulticaster
  • PalObjectEvent
  • PalObjectListener
  • PalObjectListener.EventGenerator
  • ParameterEvent
  • Parameterized
  • Parameterized.Null
  • Parameterized.ParameterizedBase
  • Parameterized.ParameterizedUser
  • Parameterized.Utils
  • ParameterizedDoubleBundle
  • ParameterizedNeoWrapper
  • ParameterizedTree
  • ParameterizedTree.Factory
  • ParameterizedTree.ParameterizedTreeBase
  • ParentableConstrainedNode
  • ParetoDistribution
  • PatternInfo
  • PenalizedLikelihood
  • PivotNode
  • PositionedNode
  • PositiveSelectionRateMatrixGroup
  • ProbabilityIterator
  • ProbabilityIterator.Factory
  • ProbabilityIterator.Utils
  • Ranker
  • RateDistribution
  • RateHandler
  • RateHandler.Utils
  • RateMatrix
  • RateMatrixGroup
  • RateMatrixHandler
  • RateMatrixUtils
  • ReadAlignment
  • ReadAlignmentOld
  • ReadDistanceMatrix
  • ReadTree
  • ReleaseInfo
  • RELLTopologyPool
  • ReplicateLikelihoodEvaluator
  • ReplicateLikelihoodEvaluator.Utils
  • Report
  • RootAccess
  • RootedTreeInterface
  • RootedTreeInterface.Instructee
  • RootedTreeInterface.RBranch
  • RootedTreeInterface.RNode
  • RootedTreeInterface.Utils
  • RootedTreeUtils
  • SampleInformation
  • SampleInformation.Factory
  • SaturatedSingleSplitDistribution
  • SearchEngine
  • SearcherUtils
  • SearchMonitor
  • SearchMonitor.Utils
  • SequencePairLikelihood
  • SequenceSimulator
  • SerialCoalescentGenerator
  • SerialCoalescentGenerator.Results
  • SerialCoalescentSimulator
  • ShimodairaHasegawaStatistics
  • ShimodairaHasegawaTest
  • SimpleAlignment
  • SimpleAnnotatedAlignment
  • SimpleCharacterAlignment
  • SimpleDataType
  • SimpleIdGroup
  • SimpleLeafCalculator
  • SimpleLHCalculator
  • SimpleLikelihoodCalculator
  • SimpleModelFastFourStateLHCalculator
  • SimpleMolecularClockLikelihoodModel
  • SimpleNode
  • SimpleRateMatrixGroup
  • SimpleSummarizable
  • SimpleTree
  • SimpleUnconstrainedLikelihoodModel
  • SimpleUnconstrainedLikelihoodModel.InternalImpl
  • SimpleUnconstrainedLikelihoodModel.LeafImpl
  • SimulatedAlignment
  • SimulatedAlignment.Factory
  • SingleClassSubstitutionModel
  • SingleSplitDistribution
  • SingleSplitMolecularClockLikelihoodModel
  • SiteDetails
  • SiteDetails.Utils
  • SitePattern
  • SkylinePlot
  • SpecificAminoAcids
  • SplitSystem
  • SplitUtils
  • SRDTGlobalClockModel
  • StateProvider
  • StateRemover
  • SteppedMutationRate
  • StoppingCriteria
  • StoppingCriteria.Factory
  • StoppingCriteria.Utils
  • StrippedAlignment
  • StrippedAnnotatedAlignment
  • SubstitutionModel
  • SubstitutionModel.Utils
  • SubstitutionTool
  • Summarizable
  • SUPGMABase
  • SUPGMABase.CISummary
  • SUPGMABase.PopulationParameters
  • SUPGMADistanceMatrix
  • SUPGMATree
  • TableReport
  • TemporalModelChange
  • TemporalModelChange.Utils
  • ThetaHandler
  • ThetaHandler.Utils
  • ThreeNumberSort
  • TimeOrderCharacterData
  • TimeStamp
  • TN
  • TOCDSampleInformation
  • TopologyTestEngine
  • TopologyTestEngine.StatisticsHandler
  • TopologyTestEngine.TestResult
  • TopologyTestEngine.TopologyPool
  • TransitionPenaltyTable
  • TransitionProbability
  • Tree
  • Tree.TreeBase
  • TreeComponent
  • TreeDistanceMatrix
  • TreeGenerator
  • TreeGenerator.Utils
  • TreeIterator
  • TreeManipulator
  • TreeManipulator.BranchAccess
  • TreeManipulator.PALBranchWrapper
  • TreeManipulator.PALNodeWrapper
  • TreeOperation
  • TreeOperation.Utils
  • TreePainter
  • TreePainterCircular
  • TreePainterNormal
  • TreeParseException
  • TreeRestricter
  • TreeSearchTool
  • TreeTool
  • TreeUtils
  • TwoStateModel
  • TwoStates
  • UnconstrainedLikelihoodModel
  • UnconstrainedLikelihoodModel.External
  • UnconstrainedLikelihoodModel.Instance
  • UnconstrainedLikelihoodModel.Internal
  • UnconstrainedLikelihoodModel.Leaf
  • UnconstrainedModel
  • UnconstrainedTree
  • UndoableAction
  • UndoableAction.Utils
  • UniformRate
  • Units
  • UnitsProvider
  • UnivariateFunction
  • UnivariateMinimum
  • UnrootedMLSearcher
  • UnrootedMLSearcher.StateObject
  • UnrootedTreeInterface
  • UnrootedTreeInterface.BaseBranch
  • UnrootedTreeInterface.GeneralBranch
  • UnrootedTreeInterface.Instructee
  • UnrootedTreeInterface.UBranch
  • UnrootedTreeInterface.UNode
  • UnrootedTreeInterface.Utils
  • UPGMATree
  • UrnModel
  • Utils
  • VariableIndependentSingleSplitDistribution
  • Version
  • VT
  • WAG
  • WindowedMutationRate
  • XMLConstants
  • XmlParseException
  • YangCodonModel
  • YangCodonModel.SimpleNeutralSelection
  • YangCodonModel.SimplePositiveSelection
  • YangCodonModel.Utils