Class Hierarchy
- java.lang.Object
- 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.substmodel.CachedRateMatrix (implements pal.misc.PalObjectListener, pal.substmodel.RateMatrix)
- pal.substmodel.ConstantIndependentSingleSplitDistribution (implements pal.substmodel.SingleSplitDistribution)
- pal.substmodel.GeneralPoissonRateMatrix (implements pal.substmodel.NeoRateMatrix)
- pal.substmodel.GeneralREVRateMatrix (implements pal.substmodel.NeoRateMatrix)
- pal.substmodel.MatrixExponential (implements java.lang.Cloneable, java.io.Serializable)
- pal.substmodel.MultiRateMatrixHandler (implements pal.misc.NeoParameterized, java.io.Serializable)
- pal.substmodel.NeutralSelectionRateMatrixGroup (implements pal.substmodel.RateMatrixGroup)
- pal.misc.PalObjectListener.EventGenerator
- 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.ParameterizedUser
- pal.substmodel.PositiveSelectionRateMatrixGroup (implements pal.substmodel.RateMatrixGroup)
- pal.substmodel.RateMatrixHandler (implements pal.misc.Parameterized, java.io.Serializable)
- pal.substmodel.RateMatrixUtils
- pal.substmodel.SaturatedSingleSplitDistribution (implements pal.substmodel.SingleSplitDistribution)
- pal.substmodel.SequenceSimulator
- pal.substmodel.SimpleRateMatrixGroup (implements pal.substmodel.RateMatrixGroup)
- pal.substmodel.SubstitutionModel.Utils
- pal.substmodel.SubstitutionTool
- pal.substmodel.TemporalModelChange.Utils
- pal.substmodel.VariableIndependentSingleSplitDistribution (implements pal.substmodel.SingleSplitDistribution)
- pal.substmodel.YangCodonModel.Utils
- pal.substmodel.AbstractRateMatrix (implements pal.misc.ExternalParameterListener, pal.substmodel.RateMatrix)
Interface Hierarchy
- 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.misc.NeoParameterized
- pal.substmodel.SingleSplitDistribution
- pal.misc.Parameterized
- pal.misc.NamedParameterized
- pal.substmodel.RateMatrix (also extends java.lang.Cloneable, pal.misc.Report, java.io.Serializable)
- pal.substmodel.SubstitutionModel (also extends pal.misc.Report, java.io.Serializable)
- pal.misc.NamedParameterized
- pal.misc.Report
- 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)
- java.io.Serializable
- pal.substmodel.AminoAcidModelID
- pal.substmodel.NeoRateMatrix
- pal.substmodel.NucleotideModelID
- pal.substmodel.RateMatrix (also extends java.lang.Cloneable, pal.misc.NamedParameterized, pal.misc.Report)
- pal.substmodel.RateMatrixGroup
- pal.substmodel.SubstitutionModel (also extends pal.misc.Parameterized, pal.misc.Report)
- pal.substmodel.TemporalModelChange
- pal.substmodel.TransitionProbability (also extends java.lang.Cloneable)