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AbstractAlignment
AbstractRateMatrix
Alignment
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AlignmentParseException
AlignmentUtils
AminoAcidAlignment
AminoAcidModel
AminoAcidModelID
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AnnotationAlignment
Attribute
AttributeNode
Binomial
BLOSUM62
BootstrappedAlignment
BootstrapStatistics
BoundsCheckedFunction
BranchLimits
CachedRateMatrix
CharacterAlignment
ChiSquareDistribution
ChiSquareTest
ChiSquareValue
CircularGraphics
ClockTree
CoalescentException
CoalescentIntervals
CoalescentSimulator
CoalescentTree
CodonAlignment
CodonModel
Codons
CodonTable
CodonTableFactory
CodonTableUtils
Comparable
ComparableDouble
Comparator
ConcatenatedAlignment
ConcatenatedAnnotatedAlignment
ConjugateDirectionSearch
ConjugateGradientSearch
ConstantMutationRate
ConstantPopulation
ConstExpGrowth
ContigencyTable
CPREV
DataType
DataTypeUtils
DatedTipsClockTree
Dayhoff
DefaultCache
DemographicClockTree
DemographicLikelihoodValue
DemographicModel
DemographicTree
DemographicValue
DifferentialEvolution
DiscreteStatistics
DistanceMatrix
DistanceMatrixUtils
DistanceParseException
DoubleKey
DoubleKeyCache
ElementFactory
ElementParser
ErrorFunction
ExpandingPopulation
ExponentialDistribution
ExponentialGrowth
ExternalParameterListener
F81
F84
FastLikelihoodCalculator
FisherExact
FormattedInput
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GammaDistribution
GammaFunction
GammaRates
GapBalancedAlignment
GeneralizedCodons
GeneralizedDEOptimizer
Genotype
GTR
HeapSort
HKY
Identifier
IdGenerator
IdGroup
IndelAlignment
IndelAnnotatedAlignment
InputSource
IntervalsExtractor
InvariableSites
IUPACNucleotides
IUPACPenaltyTable
JTT
JukesCantorDistanceMatrix
JumbledAlignment
KishinoHasegawaTest
LabelMapping
LayoutTracker
LikelihoodCalculator
LikelihoodRatioTest
LikelihoodValue
LineFunction
LinkageDisequilibrium
LinkageDisequilibriumComponent
Local
Log
Logger
LogParameterizedTree
MachineAccuracy
MathUtils
MatrixExponential
MersenneTwisterFast
MFWithGradient
ModelParameters
ModelSupport
MTREV24
MultiLocusAnnotatedAlignment
MultivariateFunction
MultivariateMinimum
MutationRateModel
MutationRateModelTree
Nameable
NameColouriser
NamedParameterized
NeighborJoiningTree
Node
NodeFactory
NodeUtils
NormalDistribution
NucleotideModel
NucleotideModelID
Nucleotides
NumericalDerivative
NumericDataType
OrthogonalLineFunction
OrthogonalSearch
OutputTarget
Painter
PairwiseDistance
PalEventMulticaster
PalObjectEvent
PalObjectListener
ParameterEvent
Parameterized
ParameterizedDouble
ParameterizedTree
ParetoDistribution
PenalizedLikelihood
PositionedNode
RateDistribution
RateMatrix
RateMatrixUtils
ReadAlignment
ReadDistanceMatrix
ReadTree
ReleaseInfo
Report
RootedTreeUtils
SequencePairLikelihood
SerialCoalescentSimulator
ShimodairaHasegawaTest
SimpleAlignment
SimpleAnnotatedAlignment
SimpleCharacterAlignment
SimpleDataType
SimpleIdGroup
SimpleLikelihoodCalculator
SimpleNode
SimpleSubstitutionModel
SimpleSummarizable
SimpleTree
SimulatedAlignment
SitePattern
SkylinePlot
SplitSystem
SplitUtils
StateRemover
SteppedMutationRate
StochasticOSearch
StrippedAlignment
StrippedAnnotatedAlignment
SubstitutionModel
Summarizable
SUPGMADistanceMatrix
SUPGMATree
TableReport
ThreeNumberSort
TimeOrderCharacterData
TimeStamp
TN
TransitionPenaltyTable
Tree
TreeComponent
TreeDistanceMatrix
TreePainter
TreePainterCircular
TreePainterNormal
TreeParseException
TreeUtils
TwoStateModel
TwoStates
UnconstrainedTree
UniformRate
Units
UnivariateFunction
UnivariateMinimum
UPGMATree
UrnModel
Utils
Version
VT
WAG
WindowedMutationRate
XMLConstants
XmlParseException
YangCodonModel