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Hierarchy For Package pal.substmodel
Package Hierarchies:
All Packages
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.
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.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
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.
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)
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