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
BLOSUM62
Binomial
BootstrapStatistics
BootstrappedAlignment
BoundsCheckedFunction
BranchAccess
BranchAccess.Utils
BranchLimits
CPREV
CachedRateMatrix
CharacterAlignment
ChiSquareDistribution
ChiSquareTest
ChiSquareValue
CircularGraphics
CladeSystem
ClassDistribution
ClockTree
ClusterTree
ClusterTree.ClusteringMethod
CoalescentException
CoalescentIntervals
CoalescentSimulator
CoalescentTree
CodonModel
CodonTable
CodonTableFactory
CodonTableUtils
Codons
Comparable
ComparableDouble
Comparator
ConcatenatedAlignment
ConcatenatedAnnotatedAlignment
ConditionalProbabilityStore
ConditionalProbabilityStore.ExtraProcessor
ConjugateDirectionSearch
ConjugateGradientSearch
ConstExpConst
ConstExpGrowth
ConstantIndependentSingleSplitDistribution
ConstantMutationRate
ConstantPopulation
Constants
ConstrainedInternalNode
ConstrainedLeafNode
ConstrainedNode
ConstrainedNode.HeightAdjustment
ConstraintModel
ConstraintModel.GroupManager
ContigencyTable
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
GTR
GammaDistribution
GammaFunction
GammaRates
GapBalanced
GapBalancedAlignment
GeneralConstraintGroupManager
GeneralConstraintGroupManager.LikelihoodScoreAccess
GeneralConstraintGroupManager.Store
GeneralConstructionTool
GeneralLikelihoodCalculator
GeneralLikelihoodSearcher
GeneralObjectState
GeneralOptimisable
GeneralPoissonRateMatrix
GeneralREVRateMatrix
GeneralRateDistributionSubstitutionModel
GeneralTopologyPool
GeneralTreeComponent
GeneralizedDEOptimizer
Genotype
GlobalClockModel
GroupLeader
HKY
HeapSort
HeightInformationUser
IUPACNucleotides
IUPACPenaltyTable
IdGenerator
IdGroup
IdGroup.Utils
Identifier
IndelAlignment
IndelAnnotatedAlignment
IndividualParameterHandler
IndividualParameterHandler.Listener
IndividualParameterHandler.Utils
InputSource
IntervalsExtractor
InvariableSites
JTT
JukesCantorDistanceMatrix
JumbledAlignment
KishinoHasegawaTest
LHCalculator
LHCalculator.AbstractExternal
LHCalculator.External
LHCalculator.Factory
LHCalculator.Generator
LHCalculator.Internal
LHCalculator.Leaf
LMSSolver
LMSSolver.Utils
LabelDisplayer
LabelDisplayer.Utils
LabelMapping
LabelMapping.Relabeller
LayoutTracker
LikelihoodCalculator
LikelihoodEvaluator
LikelihoodEvaluator.MLResult
LikelihoodEvaluator.SimpleMLResult
LikelihoodEvaluator.Utils
LikelihoodOptimiser
LikelihoodRatioTest
LikelihoodSummary
LikelihoodTool
LikelihoodValue
LineFunction
LinkageDisequilibrium
LinkageDisequilibriumComponent
Local
Log
LogParameterizedTree
Logger
MFWithGradient
MRDTGlobalClockModel
MTREV24
MachineAccuracy
Markable
MathUtils
Matrix
MatrixExponential
MersenneTwisterFast
MinimiserMonitor
MinimiserMonitor.Utils
ModelParameters
ModelSupport
MolecularClockLikelihoodModel
MolecularClockLikelihoodModel.External
MolecularClockLikelihoodModel.HeightConverter
MolecularClockLikelihoodModel.Instance
MolecularClockLikelihoodModel.Internal
MolecularClockLikelihoodModel.Leaf
MolecularClockLikelihoodModel.Simulator
MolecularDataType
MolecularDataType.Utils
MultiLocusAnnotatedAlignment
MultiParameterized
MultiParameterized.ParameterAccessWatcher
MultiRateMatrixHandler
MultivariateFunction
MultivariateMinimum
MultivariateMinimum.Factory
MutableDouble
MutationRateModel
MutationRateModel.Factory
MutationRateModelTree
NameColouriser
Nameable
NamedParameterized
NeighborJoiningTree
NeoParameterized
NeoRateMatrix
NeutralSelectionRateMatrixGroup
NexusParseException
NexusTokenizer
Node
NodeAccess
NodeFactory
NodeUtils
NormalDistribution
NucleotideModel
NucleotideModelID
Nucleotides
NumericDataType
NumericalDerivative
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
RELLTopologyPool
Ranker
RateDistribution
RateHandler
RateHandler.Utils
RateMatrix
RateMatrixGroup
RateMatrixHandler
RateMatrixUtils
ReadAlignment
ReadAlignmentOld
ReadDistanceMatrix
ReadTree
ReleaseInfo
ReplicateLikelihoodEvaluator
ReplicateLikelihoodEvaluator.Utils
Report
RootAccess
RootedTreeInterface
RootedTreeInterface.Instructee
RootedTreeInterface.RBranch
RootedTreeInterface.RNode
RootedTreeInterface.Utils
RootedTreeUtils
SRDTGlobalClockModel
SUPGMABase
SUPGMABase.CISummary
SUPGMABase.PopulationParameters
SUPGMADistanceMatrix
SUPGMATree
SampleInformation
SampleInformation.Factory
SaturatedSingleSplitDistribution
SearchEngine
SearchMonitor
SearchMonitor.Utils
SearcherUtils
SequencePairLikelihood
SequenceSimulator
SerialCoalescentGenerator
SerialCoalescentGenerator.Results
SerialCoalescentSimulator
ShimodairaHasegawaStatistics
ShimodairaHasegawaTest
SimpleAlignment
SimpleAnnotatedAlignment
SimpleCharacterAlignment
SimpleDataType
SimpleIdGroup
SimpleLHCalculator
SimpleLeafCalculator
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
StateProvider
StateRemover
SteppedMutationRate
StoppingCriteria
StoppingCriteria.Factory
StoppingCriteria.Utils
StrippedAlignment
StrippedAnnotatedAlignment
SubstitutionModel
SubstitutionModel.Utils
SubstitutionTool
Summarizable
TN
TOCDSampleInformation
TableReport
TemporalModelChange
TemporalModelChange.Utils
ThetaHandler
ThetaHandler.Utils
ThreeNumberSort
TimeOrderCharacterData
TimeStamp
TopologyTestEngine
TopologyTestEngine.StatisticsHandler
TopologyTestEngine.TestResult
TopologyTestEngine.TopologyPool
TransitionPenaltyTable
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
UPGMATree
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
UrnModel
Utils
VT
VariableIndependentSingleSplitDistribution
Version
WAG
WindowedMutationRate
XMLConstants
XmlParseException
YangCodonModel
YangCodonModel.SimpleNeutralSelection
YangCodonModel.SimplePositiveSelection
YangCodonModel.Utils
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