Hierarchy For Package pal.substmodel

Package Hierarchies:

All Packages

Class Hierarchy

• class java.lang.Object
  • 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.substmodel.CachedRateMatrix (implements pal.misc.PalObjectListener, pal.substmodel.RateMatrix)
  • class pal.substmodel.ConstantIndependentSingleSplitDistribution (implements pal.substmodel.SingleSplitDistribution)
  • class pal.substmodel.GeneralPoissonRateMatrix (implements pal.substmodel.NeoRateMatrix)
  • class pal.substmodel.GeneralREVRateMatrix (implements pal.substmodel.NeoRateMatrix)
  • class pal.substmodel.MatrixExponential (implements java.lang.Cloneable, java.io.Serializable)
  • class pal.substmodel.MultiRateMatrixHandler (implements pal.misc.NeoParameterized, java.io.Serializable)
  • class pal.substmodel.NeutralSelectionRateMatrixGroup (implements pal.substmodel.RateMatrixGroup)
  • class pal.misc.PalObjectListener.EventGenerator
    • 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.substmodel.PositiveSelectionRateMatrixGroup (implements pal.substmodel.RateMatrixGroup)
  • class pal.substmodel.RateMatrixHandler (implements pal.misc.Parameterized, java.io.Serializable)
  • class pal.substmodel.RateMatrixUtils
  • class pal.substmodel.SaturatedSingleSplitDistribution (implements pal.substmodel.SingleSplitDistribution)
  • class pal.substmodel.SequenceSimulator
  • class pal.substmodel.SimpleRateMatrixGroup (implements pal.substmodel.RateMatrixGroup)
  • class pal.substmodel.SubstitutionModel.Utils
  • class pal.substmodel.SubstitutionTool
  • class pal.substmodel.TemporalModelChange.Utils
  • class pal.substmodel.VariableIndependentSingleSplitDistribution (implements pal.substmodel.SingleSplitDistribution)
  • class pal.substmodel.YangCodonModel.Utils

Interface Hierarchy

• 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.misc.NeoParameterized
  • interface pal.substmodel.SingleSplitDistribution
• interface pal.misc.Parameterized
  • interface pal.misc.NamedParameterized
    • interface pal.substmodel.RateMatrix (also extends java.lang.Cloneable, pal.misc.Report, java.io.Serializable)
  • interface pal.substmodel.SubstitutionModel (also extends pal.misc.Report, java.io.Serializable)
• interface pal.misc.Report
  • 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 java.io.Serializable
  • interface pal.substmodel.AminoAcidModelID
  • interface pal.substmodel.NeoRateMatrix
  • 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.substmodel.SubstitutionModel (also extends pal.misc.Parameterized, pal.misc.Report)
  • interface pal.substmodel.TemporalModelChange