pal.substmodel
Interfaces 
AminoAcidModelID
ClassDistribution
NeoRateMatrix
NucleotideModelID
RateMatrix
RateMatrixGroup
SingleSplitDistribution
SubstitutionModel
TemporalModelChange
Classes 
AbstractRateMatrix
AminoAcidModel
BLOSUM62
CachedRateMatrix
CodonModel
ConstantIndependentSingleSplitDistribution
CPREV
Dayhoff
F81
F84
GammaRates
GeneralPoissonRateMatrix
GeneralRateDistributionSubstitutionModel
GeneralREVRateMatrix
GTR
HKY
InvariableSites
JTT
MatrixExponential
MTREV24
MultiRateMatrixHandler
NeutralSelectionRateMatrixGroup
NucleotideModel
PositiveSelectionRateMatrixGroup
RateDistribution
RateMatrixHandler
RateMatrixUtils
SaturatedSingleSplitDistribution
SequenceSimulator
SimpleRateMatrixGroup
SingleClassSubstitutionModel
SubstitutionModel.Utils
SubstitutionTool
TemporalModelChange.Utils
TN
TwoStateModel
UniformRate
VariableIndependentSingleSplitDistribution
VT
WAG
YangCodonModel
YangCodonModel.SimpleNeutralSelection
YangCodonModel.SimplePositiveSelection
YangCodonModel.Utils