Alignment
AlignmentException
Ambiguous
AncestralException
AncestralJoint
AncestralJointBB
AncestralJointDP
AncestralMarginal
Array1D
Array2D
ArrayMap
Branch
Calculator
Calculator.SiteCalculator
CommentedFileReader
CompiledFunction
CompiledFunction.Add
CompiledFunction.Constant
CompiledFunction.Divide
CompiledFunction.Function
CompiledFunction.Multiply
CompiledFunction.Power
CompiledFunction.Subtract
CompiledFunction.Variable
ConfidenceInterval
Constrainer
DaemonThreadFactory
Distributions
Distributions.Calculation
Distributions.DistributionsException
DNAModelFactory
DuplicationAlignment
DuplicationModelFactory
EigenvalueDecomposition
Example
FastaAlignment
FunctionParser
Gamma
GeLL
GeneralException
GeneralException.Debug
GoldenSection
GoldenSection.ProgressLevel
HypothesisTest
InputException
Likelihood
Likelihood.LikelihoodException
Likelihood.NodeLikelihood
Likelihood.RateLikelihood
Likelihood.SiteLikelihood
LUDecomposition
MapUtils
MathsParse
Model
NelderMead
NelderMead.DebugLevel
NoConstraints
NoSuchFunction
NoSuchVariable
Optimizer
Optimizer.OptimizerException
OutputException
Parameter
Parameter.FormatException
Parameters
PhylipAlignment
PossibleSettings
Probabilities
Range
RateCategory
RateCategory.FrequencyType
SequenceAlignment
SetSettings
SettingException
Settings
SetUtils
SetUtils.SetHasMultipleElementsException
Simulate
Site
SiteConstraints
SquareMatrix
SquareMatrix.Calculation
TimePassed
ToDoubleHashMap
Tree
TreeException
TreeFigure
UnexpectedError
WrongNumberOfVariables
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