Hierarchy For All Packages

Package Hierarchies:

pal.algorithmics, pal.alignment, pal.coalescent, pal.datatype, pal.distance, pal.eval, pal.gui, pal.io, pal.math, pal.mep, pal.misc, pal.popgen, pal.statistics, pal.substmodel, pal.supgma, pal.tree, pal.treesearch, pal.util, pal.xml

Class Hierarchy

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

Interface Hierarchy

• interface pal.util.AlgorithmCallback
• interface pal.alignment.AlignmentGenerator
• interface pal.alignment.AlignmentReceiver
• interface pal.algorithmics.Assessor
• interface pal.treesearch.BranchAccess
• interface pal.misc.BranchLimits
• interface pal.substmodel.ClassDistribution
• interface java.lang.Cloneable
  • interface pal.substmodel.RateMatrix (also extends pal.misc.NamedParameterized, pal.misc.Report, java.io.Serializable)
• interface pal.tree.ClusterTree.ClusteringMethod
• interface pal.coalescent.CoalescentTree
• interface java.lang.Comparable
  • interface pal.util.DoubleKey
• interface pal.util.Comparable
• interface pal.util.Comparator
• interface pal.eval.ConditionalProbabilityStore.ExtraProcessor
• interface pal.treesearch.Constants
• interface pal.treesearch.ConstrainedNode.HeightAdjustment
• interface pal.treesearch.ConstraintModel
• interface pal.treesearch.ConstraintModel.GroupManager
• interface pal.coalescent.DemographicTree
• interface pal.distance.DistanceMatrixAccess
• interface pal.distance.DistanceMatrixGenerator
• interface pal.util.DoubleKeyCache
• interface pal.misc.ExternalParameterListener
• interface pal.treesearch.GeneralConstraintGroupManager.LikelihoodScoreAccess
• interface pal.treesearch.GeneralOptimisable
• interface pal.treesearch.GeneralTreeComponent
  • interface pal.treesearch.ConstrainedNode
  • interface pal.treesearch.FreeNode
• interface pal.treesearch.GroupLeader
• interface pal.misc.IndividualParameterHandler.Listener
• interface pal.gui.LabelDisplayer
• interface pal.misc.LabelMapping.Relabeller
• interface pal.eval.LHCalculator
• interface pal.eval.LHCalculator.Internal
• interface pal.eval.LHCalculator.Leaf
• interface pal.eval.LikelihoodCalculator
• interface pal.statistics.LikelihoodEvaluator
• interface pal.statistics.LikelihoodEvaluator.MLResult
• interface pal.math.LMSSolver
• interface pal.util.Logger
• interface pal.algorithmics.Markable
• interface pal.math.MinimiserMonitor
• interface pal.eval.MolecularClockLikelihoodModel
• interface pal.eval.MolecularClockLikelihoodModel.External
• interface pal.eval.MolecularClockLikelihoodModel.HeightConverter
• interface pal.eval.MolecularClockLikelihoodModel.Internal
• interface pal.eval.MolecularClockLikelihoodModel.Leaf
• interface pal.eval.MolecularClockLikelihoodModel.Simulator
• interface pal.misc.MultiParameterized.ParameterAccessWatcher
• interface pal.math.MultivariateFunction
  • interface pal.math.MFWithGradient
• interface pal.math.MultivariateMinimum.Factory
• interface pal.mep.MutationRateModel.Factory
• interface pal.misc.Nameable
• interface pal.misc.NeoParameterized
  • interface pal.substmodel.SingleSplitDistribution
• interface pal.treesearch.NodeAccess
• interface pal.algorithmics.ObjectState
• interface pal.math.OrderEnumerator
• interface pal.math.OrderEnumerator.OEFactory
• interface pal.math.OrthogonalHints
• interface pal.math.OrthogonalSearch.RoundOptimiser
• interface pal.gui.Painter
• interface pal.misc.PalObjectListener
• interface pal.misc.Parameterized
  • interface pal.mep.DeltaModel.Instance (also extends java.io.Serializable)
  • interface pal.misc.NamedParameterized
    • interface pal.substmodel.RateMatrix (also extends java.lang.Cloneable, pal.misc.Report, java.io.Serializable)
  • interface pal.tree.ParameterizedTree (also extends pal.tree.Tree)
  • interface pal.substmodel.SubstitutionModel (also extends pal.misc.Report, java.io.Serializable)
• interface pal.tree.ParameterizedTree.Factory
• interface pal.treesearch.ParentableConstrainedNode
• interface pal.algorithmics.ProbabilityIterator
• interface pal.algorithmics.ProbabilityIterator.Factory
• interface pal.supgma.RateHandler
• interface pal.statistics.ReplicateLikelihoodEvaluator
• interface pal.misc.Report
  • interface pal.alignment.AnnotationAlignment (also extends pal.alignment.Alignment)
  • interface pal.alignment.CharacterAlignment (also extends pal.misc.IdGroup, java.io.Serializable, pal.misc.TableReport)
  • interface pal.substmodel.RateMatrix (also extends java.lang.Cloneable, pal.misc.NamedParameterized, java.io.Serializable)
  • interface pal.substmodel.SubstitutionModel (also extends pal.misc.Parameterized, java.io.Serializable)
• interface pal.treesearch.RootAccess
• interface pal.tree.RootedTreeInterface
• interface pal.tree.RootedTreeInterface.Instructee
• interface pal.tree.RootedTreeInterface.RBranch
• interface pal.tree.RootedTreeInterface.RNode
• interface pal.misc.SampleInformation
• interface pal.misc.SampleInformation.Factory
• interface pal.treesearch.SearchMonitor
• interface java.io.Serializable
  • interface pal.alignment.Alignment (also extends pal.misc.IdGroup)
    • interface pal.alignment.AnnotationAlignment (also extends pal.misc.Report)
  • interface pal.substmodel.AminoAcidModelID
  • interface pal.alignment.CharacterAlignment (also extends pal.misc.IdGroup, pal.misc.Report, pal.misc.TableReport)
  • interface pal.datatype.CodonTable
  • interface pal.datatype.DataType
    • interface pal.datatype.AmbiguousDataType
    • interface pal.datatype.MolecularDataType
  • interface pal.mep.DeltaModel
  • interface pal.mep.DeltaModel.Instance (also extends pal.misc.Parameterized)
  • interface pal.misc.IdGroup
    • interface pal.alignment.Alignment (also extends java.io.Serializable)
      • interface pal.alignment.AnnotationAlignment (also extends pal.misc.Report)
    • interface pal.alignment.CharacterAlignment (also extends pal.misc.Report, java.io.Serializable, pal.misc.TableReport)
    • interface pal.tree.Tree (also extends java.io.Serializable, pal.misc.Units, pal.misc.UnitsProvider)
      • interface pal.tree.ParameterizedTree (also extends pal.misc.Parameterized)
  • interface pal.misc.IndividualParameterHandler
  • interface pal.eval.LHCalculator.External
  • interface pal.eval.LHCalculator.Factory
  • interface pal.eval.LHCalculator.Generator
  • interface pal.eval.MolecularClockLikelihoodModel.Instance
  • interface pal.substmodel.NeoRateMatrix
  • interface pal.tree.Node
    • interface pal.tree.AttributeNode
  • interface pal.substmodel.NucleotideModelID
  • interface pal.substmodel.RateMatrix (also extends java.lang.Cloneable, pal.misc.NamedParameterized, pal.misc.Report)
  • interface pal.substmodel.RateMatrixGroup
  • interface pal.algorithmics.StoppingCriteria
  • interface pal.algorithmics.StoppingCriteria.Factory
  • interface pal.substmodel.SubstitutionModel (also extends pal.misc.Parameterized, pal.misc.Report)
  • interface pal.misc.Summarizable
  • interface pal.substmodel.TemporalModelChange
  • interface pal.tree.Tree (also extends pal.misc.IdGroup, pal.misc.Units, pal.misc.UnitsProvider)
    • interface pal.tree.ParameterizedTree (also extends pal.misc.Parameterized)
  • interface pal.eval.UnconstrainedLikelihoodModel.External
  • interface pal.eval.UnconstrainedLikelihoodModel.Instance
• interface pal.eval.SiteDetails
• interface pal.algorithmics.StateProvider
• interface pal.supgma.SUPGMABase.CISummary
• interface pal.supgma.SUPGMABase.PopulationParameters
• interface pal.misc.TableReport
  • interface pal.alignment.CharacterAlignment (also extends pal.misc.IdGroup, pal.misc.Report, java.io.Serializable)
• interface pal.supgma.ThetaHandler
• interface pal.statistics.TopologyTestEngine.StatisticsHandler
• interface pal.statistics.TopologyTestEngine.TestResult
• interface pal.statistics.TopologyTestEngine.TopologyPool
• interface pal.datatype.TransitionPenaltyTable
• interface pal.tree.TreeGenerator
  • interface pal.tree.TreeIterator
• interface pal.tree.TreeManipulator.BranchAccess
• interface pal.tree.TreeOperation
• interface pal.eval.UnconstrainedLikelihoodModel
• interface pal.eval.UnconstrainedLikelihoodModel.Internal
• interface pal.eval.UnconstrainedLikelihoodModel.Leaf
• interface pal.algorithmics.UndoableAction
• interface pal.misc.Units
  • interface pal.tree.Tree (also extends pal.misc.IdGroup, java.io.Serializable, pal.misc.UnitsProvider)
    • interface pal.tree.ParameterizedTree (also extends pal.misc.Parameterized)
  • interface pal.misc.UnitsProvider
    • interface pal.tree.Tree (also extends pal.misc.IdGroup, java.io.Serializable, pal.misc.Units)
      • interface pal.tree.ParameterizedTree (also extends pal.misc.Parameterized)
• interface pal.math.UnivariateFunction
• interface pal.tree.UnrootedTreeInterface
• interface pal.tree.UnrootedTreeInterface.GeneralBranch
  • interface pal.tree.UnrootedTreeInterface.BaseBranch
  • interface pal.tree.UnrootedTreeInterface.UBranch
• interface pal.tree.UnrootedTreeInterface.Instructee
• interface pal.tree.UnrootedTreeInterface.UNode
• interface pal.util.XMLConstants