All Classes
Adapter
AIC
Alignment
AlignmentException
Ambiguous
AncestralException
AncestralJoint
AncestralJointBB
AncestralJointDP
AncestralMarginal
Array1D
Array2D
Assignment
BIC
Branch
Calculator
Calculator.CalculatorException
CommentedFileReader
CompiledFunction
CompiledFunction.Add
CompiledFunction.Constant
CompiledFunction.Divide
CompiledFunction.Function
CompiledFunction.Multiply
CompiledFunction.Power
CompiledFunction.Subtract
CompiledFunction.Variable
ConfidenceInterval
ConjugateGradient
ConjugateGradient.ProgressLevel
ConjugateGradient.Update
DaemonThreadFactory
Distributions
Distributions.Calculation
Distributions.DistributionsException
DNAModelFactory
DNAModelFactory.DNAModel
DuplicationAlignment
DuplicationModelFactory
EigenvalueDecomposition
EmpiricalAdapter
EqualAdapter
FastaAlignment
FitzJohnRoot
FunctionParser
Gamma
GeLL
GeneralException
GeneralException.Debug
GenericAlignment
GoldenSection
GoldenSection.ProgressLevel
HypothesisTest
IdentityAdapter
InputException
Likelihood
LUDecomposition
MathsParse
Model
Model.ModelException
NelderMead
NelderMead.DebugLevel
NoSuchFunction
NoSuchVariable
Optimizable
Optimizer
Optimizer.OptimizerException
OutputException
Parameter
Parameter.FormatException
Parameters
Parameters.ParameterException
PhylipAlignment
PossibleSettings
Probabilities
Range
RateCategory
RateCategory.FrequencyType
RateCategory.RateException
Real
RealFactory
RealFactory.RealType
Root
RYModelFactory
SetSettings
SettingException
Settings
SetUtils
SetUtils.SetHasMultipleElementsException
Simulate
Site
SiteLikelihood
SiteLikelihood.LikelihoodException
SiteLikelihood.NodeLikelihood
SiteLikelihood.RateLikelihood
SmallDouble
Split
SquareMatrix
SquareMatrix.Calculation
StandardCalculator
StandardDouble
StandardLikelihood
StandardRoot
TestInstance
TimePassed
Tree
TreeException
TreeFigure
UnexpectedError
UniqueSite
WrongNumberOfVariables