- 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