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