JavaScript is disabled on your browser.
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV
NEXT
FRAMES
NO FRAMES
All Classes
Hierarchy For All Packages
Package Hierarchies:
pal.algorithmics
,
pal.alignment
,
pal.coalescent
,
pal.datatype
,
pal.distance
,
pal.eval
,
pal.gui
,
pal.io
,
pal.math
,
pal.mep
,
pal.misc
,
pal.popgen
,
pal.statistics
,
pal.substmodel
,
pal.supgma
,
pal.tree
,
pal.treesearch
,
pal.util
,
pal.xml
Class Hierarchy
java.lang.Object
pal.alignment.
AbstractAlignment
(implements pal.alignment.
Alignment
, pal.misc.
IdGroup
, pal.misc.
Report
, java.io.Serializable)
pal.alignment.
BootstrappedAlignment
pal.alignment.
ConcatenatedAlignment
pal.alignment.
ConcatenatedAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
pal.alignment.
GapBalancedAlignment
(implements java.io.Serializable)
pal.alignment.
IndelAlignment
pal.alignment.
IndelAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
pal.alignment.
JumbledAlignment
pal.alignment.
ReadAlignment
pal.alignment.
ReadAlignmentOld
pal.alignment.
SimpleAlignment
pal.alignment.
MultiLocusAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
pal.alignment.
SimpleAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
pal.tree.
SimulatedAlignment
pal.alignment.
SitePattern
pal.alignment.
StrippedAlignment
pal.alignment.
StrippedAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
pal.treesearch.
AbstractLeafNode
pal.treesearch.
ConstrainedLeafNode
(implements pal.treesearch.
ConstrainedNode
)
pal.treesearch.
FreeLeafNode
(implements pal.treesearch.
FreeNode
)
pal.treesearch.
AbstractParentableConstrainedNode
(implements pal.treesearch.
ParentableConstrainedNode
)
pal.treesearch.
ConstrainedInternalNode
(implements pal.treesearch.
ConstrainedNode
, pal.treesearch.
GeneralOptimisable
)
pal.treesearch.
PivotNode
(implements pal.treesearch.
FreeNode
, pal.treesearch.
GeneralOptimisable
, pal.treesearch.
GroupLeader
, pal.treesearch.
ParentableConstrainedNode
, pal.treesearch.
RootAccess
)
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.util.
AlgorithmCallback.Utils
pal.alignment.
AlignmentBuilder
pal.alignment.
AlignmentGenerator.Utils
pal.alignment.
AlignmentReaders
pal.alignment.
AlignmentReaders.PhylipClustalAlignment
pal.alignment.
AlignmentReaders.UnalignedAlignment
pal.alignment.
AlignmentReceiver.BucketReceiver
(implements pal.alignment.
AlignmentReceiver
)
pal.alignment.
AlignmentReceiver.SingleReceiver
(implements pal.alignment.
AlignmentReceiver
)
pal.alignment.
AlignmentTool
pal.alignment.
AlignmentUtils
pal.misc.
Attribute
pal.math.
Binomial
(implements java.io.Serializable)
pal.statistics.
BootstrapStatistics
pal.math.
BoundsCheckedFunction
(implements pal.math.
MultivariateFunction
)
pal.treesearch.
BranchAccess.Utils
pal.substmodel.
CachedRateMatrix
(implements pal.misc.
PalObjectListener
, pal.substmodel.
RateMatrix
)
pal.statistics.
ChiSquareTest
pal.eval.
ChiSquareValue
(implements pal.math.
MultivariateFunction
)
pal.gui.
CircularGraphics
pal.tree.
CladeSystem
pal.coalescent.
CoalescentIntervals
(implements pal.misc.
Report
, java.io.Serializable, pal.misc.
Units
)
pal.coalescent.
CoalescentSimulator
pal.datatype.
CodonTableFactory
pal.datatype.
CodonTableUtils
pal.util.
ComparableDouble
(implements pal.util.
Comparable
)
java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
pal.gui.
LinkageDisequilibriumComponent
(implements java.awt.print.Printable)
pal.gui.
TreeComponent
pal.eval.
ConditionalProbabilityStore
(implements java.io.Serializable)
pal.substmodel.
ConstantIndependentSingleSplitDistribution
(implements pal.substmodel.
SingleSplitDistribution
)
pal.statistics.
ContigencyTable
pal.alignment.
DataTranslator
pal.datatype.
DataType.Utils
pal.datatype.
DataTypeTool
pal.util.
DefaultCache
(implements pal.util.
DoubleKeyCache
)
pal.mep.
DeltaModel.Utils
pal.coalescent.
DemographicModel
(implements java.lang.Cloneable, pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
, pal.misc.
Units
)
pal.coalescent.
ConstantPopulation
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
pal.coalescent.
ExponentialGrowth
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
pal.coalescent.
ConstExpGrowth
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable)
pal.coalescent.
ConstExpConst
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable)
pal.coalescent.
ExpandingPopulation
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable)
pal.eval.
DemographicValue
(implements pal.math.
MultivariateFunction
)
pal.statistics.
DiscreteStatistics
pal.distance.
DistanceMatrix
(implements pal.misc.
IdGroup
, java.io.Serializable)
pal.distance.
AlignmentDistanceMatrix
(implements java.io.Serializable)
pal.distance.
JukesCantorDistanceMatrix
pal.distance.
ReadDistanceMatrix
pal.supgma.
SUPGMADistanceMatrix
pal.tree.
TreeDistanceMatrix
pal.distance.
DistanceMatrixAccess.Utils
pal.distance.
DistanceMatrixGenerator.Utils
pal.distance.
DistanceMatrixUtils
(implements java.io.Serializable)
pal.distance.
DistanceTool
pal.xml.
ElementFactory
(implements pal.util.
XMLConstants
)
pal.xml.
ElementParser
(implements pal.util.
XMLConstants
)
pal.math.
ErrorFunction
pal.math.
EvaluationCounter
(implements pal.math.
MultivariateFunction
)
java.util.EventObject (implements java.io.Serializable)
pal.misc.
PalObjectEvent
pal.misc.
ParameterEvent
pal.eval.
FastFourStateLHCalculator
(implements pal.eval.
LHCalculator
)
pal.eval.
FastLikelihoodCalculator
(implements pal.eval.
LikelihoodCalculator
, pal.misc.
PalObjectListener
)
pal.statistics.
FisherExact
pal.treesearch.
FixedBSRDTGlobalClockModel
(implements pal.treesearch.
ConstraintModel
, pal.treesearch.
ConstraintModel.GroupManager
, pal.eval.
MolecularClockLikelihoodModel.HeightConverter
, pal.misc.
NeoParameterized
)
pal.treesearch.
FixedSRDTGlobalClockModel
(implements pal.treesearch.
ConstraintModel
, pal.treesearch.
ConstraintModel.GroupManager
, pal.eval.
MolecularClockLikelihoodModel.HeightConverter
)
pal.io.
FormattedInput
(implements java.io.Serializable)
pal.io.
FormattedOutput
(implements java.io.Serializable)
pal.treesearch.
FreeBranch
(implements pal.treesearch.
GeneralOptimisable
, pal.treesearch.
RootAccess
)
pal.treesearch.
FreeInternalNode
(implements pal.treesearch.
FreeNode
)
pal.statistics.
GammaDistribution
pal.statistics.
ChiSquareDistribution
pal.statistics.
ExponentialDistribution
pal.math.
GammaFunction
pal.treesearch.
GeneralConstraintGroupManager
pal.treesearch.
GeneralConstraintGroupManager.Store
pal.treesearch.
GeneralConstructionTool
pal.eval.
GeneralLikelihoodCalculator
(implements pal.eval.
LikelihoodCalculator
, pal.misc.
PalObjectListener
)
pal.treesearch.
GeneralLikelihoodSearcher
pal.algorithmics.
GeneralObjectState
(implements pal.algorithmics.
ObjectState
)
pal.substmodel.
GeneralPoissonRateMatrix
(implements pal.substmodel.
NeoRateMatrix
)
pal.substmodel.
GeneralREVRateMatrix
(implements pal.substmodel.
NeoRateMatrix
)
pal.statistics.
GeneralTopologyPool
(implements pal.statistics.
TopologyTestEngine.TopologyPool
)
pal.alignment.
Genotype
pal.treesearch.
GlobalClockModel
(implements pal.treesearch.
ConstraintModel
, pal.treesearch.
ConstraintModel.GroupManager
, pal.eval.
MolecularClockLikelihoodModel.HeightConverter
, pal.misc.
NeoParameterized
)
pal.util.
HeapSort
pal.treesearch.
HeightInformationUser
pal.misc.
Identifier
(implements pal.util.
Comparable
, pal.misc.
Nameable
, java.io.Serializable)
pal.misc.
IdGenerator
pal.misc.
IdGroup.Utils
pal.misc.
IndividualParameterHandler.Utils
pal.coalescent.
IntervalsExtractor
(implements pal.misc.
Units
)
pal.datatype.
IUPACPenaltyTable
(implements pal.datatype.
TransitionPenaltyTable
)
pal.statistics.
KishinoHasegawaTest
(implements pal.misc.
Report
)
pal.gui.
LabelDisplayer.Utils
pal.misc.
LabelMapping
(implements java.io.Serializable)
pal.gui.
LayoutTracker
pal.eval.
LHCalculator.AbstractExternal
pal.statistics.
LikelihoodEvaluator.SimpleMLResult
(implements pal.statistics.
LikelihoodEvaluator.MLResult
)
pal.statistics.
LikelihoodEvaluator.Utils
pal.eval.
LikelihoodOptimiser
pal.statistics.
LikelihoodRatioTest
pal.eval.
LikelihoodSummary
(implements java.io.Serializable)
pal.eval.
LikelihoodTool
pal.eval.
LikelihoodValue
pal.eval.
DemographicLikelihoodValue
pal.math.
LineFunction
(implements pal.math.
UnivariateFunction
)
pal.math.
LMSSolver.Utils
pal.tree.
Local
pal.util.
Log
(implements pal.util.
Logger
)
pal.math.
MachineAccuracy
pal.math.
MathUtils
pal.math.
Matrix
pal.substmodel.
MatrixExponential
(implements java.lang.Cloneable, java.io.Serializable)
pal.math.
MersenneTwisterFast
(implements java.io.Serializable)
pal.math.
MinimiserMonitor.Utils
pal.eval.
ModelParameters
(implements pal.math.
MultivariateFunction
)
pal.statistics.
ModelSupport
(implements pal.misc.
Report
)
pal.datatype.
MolecularDataType.Utils
pal.treesearch.
MRDTGlobalClockModel
(implements pal.treesearch.
ConstraintModel
, pal.treesearch.
ConstraintModel.GroupManager
, pal.eval.
MolecularClockLikelihoodModel.HeightConverter
, pal.misc.
NeoParameterized
)
pal.misc.
MultiParameterized
(implements pal.misc.
Parameterized
)
pal.substmodel.
MultiRateMatrixHandler
(implements pal.misc.
NeoParameterized
, java.io.Serializable)
pal.math.
MultivariateMinimum
pal.math.
ConjugateDirectionSearch
pal.math.
ConjugateGradientSearch
pal.math.
DifferentialEvolution
pal.math.
GeneralizedDEOptimizer
pal.math.
OrthogonalSearch
pal.misc.
MutableDouble
(implements java.io.Serializable)
pal.mep.
MutationRateModel
(implements java.lang.Cloneable, pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
, pal.misc.
Units
)
pal.mep.
ConstantMutationRate
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
pal.mep.
SteppedMutationRate
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
pal.mep.
WindowedMutationRate
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
pal.gui.
NameColouriser
(implements java.io.Serializable)
pal.substmodel.
NeutralSelectionRateMatrixGroup
(implements pal.substmodel.
RateMatrixGroup
)
pal.io.
NexusTokenizer
pal.tree.
NodeFactory
pal.tree.
NodeUtils
pal.statistics.
NormalDistribution
pal.math.
NumericalDerivative
pal.math.
OrderEnumerator.Utils
pal.math.
OrthogonalHints.Utils
pal.math.
OrthogonalLineFunction
(implements pal.math.
UnivariateFunction
)
pal.distance.
PairwiseDistance
(implements java.io.Serializable)
pal.misc.
PalEventMulticaster
pal.misc.
PalObjectListener.EventGenerator
pal.misc.
Parameterized.ParameterizedBase
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.misc.
Parameterized.Null
(implements pal.misc.
Parameterized
)
pal.misc.
Parameterized.Utils
pal.misc.
ParameterizedDoubleBundle
(implements pal.misc.
NeoParameterized
)
pal.misc.
ParameterizedNeoWrapper
(implements pal.misc.
NeoParameterized
)
pal.tree.
ParameterizedTree.ParameterizedTreeBase
(implements pal.misc.
Parameterized
, pal.tree.
Tree
)
pal.tree.
ClockTree
(implements pal.tree.
ParameterizedTree
)
pal.coalescent.
DemographicClockTree
(implements pal.coalescent.
DemographicTree
)
pal.tree.
LogParameterizedTree
(implements pal.tree.
ParameterizedTree
)
pal.tree.
MutationRateModelTree
(implements pal.math.
OrthogonalHints
, pal.tree.
ParameterizedTree
)
pal.tree.
UnconstrainedTree
(implements pal.tree.
ParameterizedTree
)
pal.statistics.
ParetoDistribution
pal.eval.
PatternInfo
pal.statistics.
PenalizedLikelihood
pal.substmodel.
PositiveSelectionRateMatrixGroup
(implements pal.substmodel.
RateMatrixGroup
)
pal.algorithmics.
ProbabilityIterator.Utils
pal.algorithmics.
Ranker
pal.supgma.
RateHandler.Utils
pal.substmodel.
RateMatrixHandler
(implements pal.misc.
Parameterized
, java.io.Serializable)
pal.substmodel.
RateMatrixUtils
java.io.Reader (implements java.io.Closeable, java.lang.Readable)
java.io.FilterReader
java.io.PushbackReader
pal.io.
InputSource
pal.misc.
ReleaseInfo
pal.statistics.
RELLTopologyPool
(implements pal.statistics.
TopologyTestEngine.TopologyPool
)
pal.statistics.
ReplicateLikelihoodEvaluator.Utils
pal.tree.
RootedTreeInterface.Utils
pal.tree.
RootedTreeUtils
pal.substmodel.
SaturatedSingleSplitDistribution
(implements pal.substmodel.
SingleSplitDistribution
)
pal.algorithmics.
SearchEngine
pal.treesearch.
SearcherUtils
pal.treesearch.
SearchMonitor.Utils
pal.distance.
SequencePairLikelihood
(implements java.io.Serializable, pal.math.
UnivariateFunction
)
pal.substmodel.
SequenceSimulator
pal.coalescent.
SerialCoalescentGenerator
(implements java.io.Serializable)
pal.coalescent.
SerialCoalescentGenerator.Results
pal.coalescent.
SerialCoalescentSimulator
(implements java.io.Serializable)
pal.statistics.
ShimodairaHasegawaStatistics
(implements pal.statistics.
TopologyTestEngine.StatisticsHandler
)
pal.statistics.
ShimodairaHasegawaTest
(implements pal.misc.
Report
)
pal.alignment.
SimpleCharacterAlignment
(implements pal.alignment.
CharacterAlignment
, pal.misc.
IdGroup
, pal.misc.
Report
, java.io.Serializable)
pal.datatype.
SimpleDataType
(implements pal.datatype.
DataType
)
pal.datatype.
AminoAcids
pal.datatype.
SpecificAminoAcids
(implements pal.datatype.
MolecularDataType
)
pal.datatype.
Codons
(implements pal.datatype.
MolecularDataType
)
pal.datatype.
GapBalanced
(implements pal.datatype.
MolecularDataType
)
pal.datatype.
IUPACNucleotides
(implements pal.datatype.
AmbiguousDataType
, pal.datatype.
MolecularDataType
)
pal.datatype.
Nucleotides
(implements pal.datatype.
MolecularDataType
)
pal.datatype.
NumericDataType
pal.datatype.
StateRemover
(implements java.io.Serializable)
pal.datatype.
TwoStates
pal.misc.
SimpleIdGroup
(implements pal.misc.
IdGroup
, pal.misc.
Nameable
, java.io.Serializable)
pal.eval.
SimpleLeafCalculator
(implements pal.eval.
LHCalculator.Leaf
)
pal.eval.
SimpleLHCalculator
(implements pal.eval.
LHCalculator
)
pal.eval.
SimpleLikelihoodCalculator
(implements pal.eval.
LikelihoodCalculator
)
pal.eval.
SimpleModelFastFourStateLHCalculator
(implements pal.eval.
LHCalculator
)
pal.eval.
SimpleMolecularClockLikelihoodModel
(implements pal.eval.
MolecularClockLikelihoodModel
)
pal.tree.
SimpleNode
(implements pal.tree.
AttributeNode
)
pal.gui.
PositionedNode
pal.substmodel.
SimpleRateMatrixGroup
(implements pal.substmodel.
RateMatrixGroup
)
pal.misc.
SimpleSummarizable
(implements java.io.Serializable, pal.misc.
Summarizable
)
pal.tree.
SimpleTree
(implements pal.misc.
Report
, java.io.Serializable, pal.tree.
Tree
, pal.misc.
Units
)
pal.tree.
ClusterTree
pal.supgma.
SUPGMATree
pal.tree.
NeighborJoiningTree
pal.tree.
ReadTree
pal.tree.
UPGMATree
pal.eval.
SimpleUnconstrainedLikelihoodModel
(implements pal.eval.
UnconstrainedLikelihoodModel
)
pal.eval.
SimpleUnconstrainedLikelihoodModel.InternalImpl
(implements pal.eval.
UnconstrainedLikelihoodModel.Internal
)
pal.eval.
SimpleUnconstrainedLikelihoodModel.LeafImpl
(implements pal.eval.
UnconstrainedLikelihoodModel.Leaf
)
pal.tree.
SimulatedAlignment.Factory
pal.eval.
SingleSplitMolecularClockLikelihoodModel
(implements pal.eval.
MolecularClockLikelihoodModel
)
pal.eval.
SiteDetails.Utils
pal.coalescent.
SkylinePlot
(implements pal.misc.
Report
, java.io.Serializable, pal.misc.
Units
)
pal.tree.
SplitSystem
pal.tree.
SplitUtils
pal.treesearch.
SRDTGlobalClockModel
(implements pal.treesearch.
ConstraintModel
, pal.treesearch.
ConstraintModel.GroupManager
, pal.eval.
MolecularClockLikelihoodModel.HeightConverter
, pal.misc.
NeoParameterized
)
pal.algorithmics.
StoppingCriteria.Utils
pal.substmodel.
SubstitutionModel.Utils
pal.substmodel.
SubstitutionTool
pal.supgma.
SUPGMABase
pal.substmodel.
TemporalModelChange.Utils
pal.supgma.
ThetaHandler.Utils
java.lang.Thread (implements java.lang.Runnable)
pal.popgen.
LinkageDisequilibrium
(implements java.io.Serializable, pal.misc.
TableReport
)
pal.util.
ThreeNumberSort
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
pal.alignment.
AlignmentParseException
pal.coalescent.
CoalescentException
pal.distance.
DistanceParseException
pal.io.
NexusParseException
pal.tree.
TreeParseException
pal.xml.
XmlParseException
pal.misc.
TimeOrderCharacterData
(implements pal.misc.
BranchLimits
, pal.misc.
IdGroup
, java.io.Serializable, pal.misc.
UnitsProvider
)
pal.misc.
TimeStamp
pal.misc.
TOCDSampleInformation
(implements pal.misc.
SampleInformation
)
pal.statistics.
TopologyTestEngine
pal.tree.
Tree.TreeBase
(implements pal.misc.
Report
, java.io.Serializable, pal.tree.
Tree
, pal.misc.
Units
)
pal.tree.
TreeGenerator.Utils
pal.tree.
TreeManipulator
(implements pal.tree.
RootedTreeInterface.Instructee
, pal.tree.
UnrootedTreeInterface.Instructee
)
pal.tree.
TreeManipulator.PALBranchWrapper
pal.tree.
TreeManipulator.PALNodeWrapper
pal.tree.
TreeOperation.Utils
pal.gui.
TreePainter
(implements pal.gui.
Painter
)
pal.gui.
TreePainterCircular
pal.gui.
TreePainterNormal
pal.tree.
TreeRestricter
pal.treesearch.
TreeSearchTool
pal.tree.
TreeTool
pal.tree.
TreeUtils
pal.treesearch.
UnconstrainedModel
(implements pal.treesearch.
ConstraintModel
)
pal.algorithmics.
UndoableAction.Utils
pal.math.
UnivariateMinimum
pal.treesearch.
UnrootedMLSearcher
(implements pal.algorithmics.
Markable
, pal.algorithmics.
StateProvider
, pal.tree.
UnrootedTreeInterface.Instructee
)
pal.treesearch.
UnrootedMLSearcher.StateObject
pal.tree.
UnrootedTreeInterface.Utils
pal.math.
UrnModel
(implements java.io.Serializable)
pal.misc.
Utils
pal.substmodel.
VariableIndependentSingleSplitDistribution
(implements pal.substmodel.
SingleSplitDistribution
)
pal.util.
Version
java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
java.io.PrintWriter
pal.io.
OutputTarget
pal.substmodel.
YangCodonModel.Utils
Interface Hierarchy
pal.util.
AlgorithmCallback
pal.alignment.
AlignmentGenerator
pal.alignment.
AlignmentReceiver
pal.algorithmics.
Assessor
pal.treesearch.
BranchAccess
pal.misc.
BranchLimits
pal.substmodel.
ClassDistribution
java.lang.Cloneable
pal.substmodel.
RateMatrix
(also extends pal.misc.
NamedParameterized
, pal.misc.
Report
, java.io.Serializable)
pal.tree.
ClusterTree.ClusteringMethod
pal.coalescent.
CoalescentTree
java.lang.Comparable<T>
pal.util.
DoubleKey
pal.util.
Comparable
pal.util.
Comparator
pal.eval.
ConditionalProbabilityStore.ExtraProcessor
pal.treesearch.
Constants
pal.treesearch.
ConstrainedNode.HeightAdjustment
pal.treesearch.
ConstraintModel
pal.treesearch.
ConstraintModel.GroupManager
pal.coalescent.
DemographicTree
pal.distance.
DistanceMatrixAccess
pal.distance.
DistanceMatrixGenerator
pal.util.
DoubleKeyCache
pal.misc.
ExternalParameterListener
pal.treesearch.
GeneralConstraintGroupManager.LikelihoodScoreAccess
pal.treesearch.
GeneralOptimisable
pal.treesearch.
GeneralTreeComponent
pal.treesearch.
ConstrainedNode
pal.treesearch.
FreeNode
pal.treesearch.
GroupLeader
pal.misc.
IndividualParameterHandler.Listener
pal.gui.
LabelDisplayer
pal.misc.
LabelMapping.Relabeller
pal.eval.
LHCalculator
pal.eval.
LHCalculator.Internal
pal.eval.
LHCalculator.Leaf
pal.eval.
LikelihoodCalculator
pal.statistics.
LikelihoodEvaluator
pal.statistics.
LikelihoodEvaluator.MLResult
pal.math.
LMSSolver
pal.util.
Logger
pal.algorithmics.
Markable
pal.math.
MinimiserMonitor
pal.eval.
MolecularClockLikelihoodModel
pal.eval.
MolecularClockLikelihoodModel.External
pal.eval.
MolecularClockLikelihoodModel.HeightConverter
pal.eval.
MolecularClockLikelihoodModel.Internal
pal.eval.
MolecularClockLikelihoodModel.Leaf
pal.eval.
MolecularClockLikelihoodModel.Simulator
pal.misc.
MultiParameterized.ParameterAccessWatcher
pal.math.
MultivariateFunction
pal.math.
MFWithGradient
pal.math.
MultivariateMinimum.Factory
pal.mep.
MutationRateModel.Factory
pal.misc.
Nameable
pal.misc.
NeoParameterized
pal.substmodel.
SingleSplitDistribution
pal.treesearch.
NodeAccess
pal.algorithmics.
ObjectState
pal.math.
OrderEnumerator
pal.math.
OrderEnumerator.OEFactory
pal.math.
OrthogonalHints
pal.math.
OrthogonalSearch.RoundOptimiser
pal.gui.
Painter
pal.misc.
PalObjectListener
pal.misc.
Parameterized
pal.mep.
DeltaModel.Instance
(also extends java.io.Serializable)
pal.misc.
NamedParameterized
pal.substmodel.
RateMatrix
(also extends java.lang.Cloneable, pal.misc.
Report
, java.io.Serializable)
pal.tree.
ParameterizedTree
(also extends pal.tree.
Tree
)
pal.substmodel.
RateMatrix
(also extends java.lang.Cloneable, pal.misc.
NamedParameterized
, pal.misc.
Report
, java.io.Serializable)
pal.substmodel.
SubstitutionModel
(also extends pal.misc.
Report
, java.io.Serializable)
pal.tree.
ParameterizedTree.Factory
pal.treesearch.
ParentableConstrainedNode
pal.algorithmics.
ProbabilityIterator
pal.algorithmics.
ProbabilityIterator.Factory
pal.supgma.
RateHandler
pal.statistics.
ReplicateLikelihoodEvaluator
pal.misc.
Report
pal.alignment.
AnnotationAlignment
(also extends pal.alignment.
Alignment
)
pal.alignment.
CharacterAlignment
(also extends pal.misc.
IdGroup
, java.io.Serializable, pal.misc.
TableReport
)
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)
pal.treesearch.
RootAccess
pal.tree.
RootedTreeInterface
pal.tree.
RootedTreeInterface.Instructee
pal.tree.
RootedTreeInterface.RBranch
pal.tree.
RootedTreeInterface.RNode
pal.misc.
SampleInformation
pal.misc.
SampleInformation.Factory
pal.treesearch.
SearchMonitor
java.io.Serializable
pal.alignment.
Alignment
(also extends pal.misc.
IdGroup
)
pal.alignment.
AnnotationAlignment
(also extends pal.misc.
Report
)
pal.datatype.
AmbiguousDataType
pal.substmodel.
AminoAcidModelID
pal.alignment.
AnnotationAlignment
(also extends pal.alignment.
Alignment
, pal.misc.
Report
)
pal.tree.
AttributeNode
pal.alignment.
CharacterAlignment
(also extends pal.misc.
IdGroup
, pal.misc.
Report
, pal.misc.
TableReport
)
pal.datatype.
CodonTable
pal.datatype.
DataType
pal.datatype.
AmbiguousDataType
pal.datatype.
MolecularDataType
pal.mep.
DeltaModel
pal.mep.
DeltaModel.Instance
(also extends pal.misc.
Parameterized
)
pal.misc.
IdGroup
pal.alignment.
Alignment
(also extends java.io.Serializable)
pal.alignment.
AnnotationAlignment
(also extends pal.misc.
Report
)
pal.alignment.
AnnotationAlignment
(also extends pal.alignment.
Alignment
, pal.misc.
Report
)
pal.alignment.
CharacterAlignment
(also extends pal.misc.
Report
, java.io.Serializable, pal.misc.
TableReport
)
pal.tree.
ParameterizedTree
(also extends pal.misc.
Parameterized
, pal.tree.
Tree
)
pal.tree.
Tree
(also extends java.io.Serializable, pal.misc.
Units
, pal.misc.
UnitsProvider
)
pal.tree.
ParameterizedTree
(also extends pal.misc.
Parameterized
)
pal.misc.
IndividualParameterHandler
pal.eval.
LHCalculator.External
pal.eval.
LHCalculator.Factory
pal.eval.
LHCalculator.Generator
pal.eval.
MolecularClockLikelihoodModel.Instance
pal.datatype.
MolecularDataType
pal.substmodel.
NeoRateMatrix
pal.tree.
Node
pal.tree.
AttributeNode
pal.substmodel.
NucleotideModelID
pal.tree.
ParameterizedTree
(also extends pal.misc.
Parameterized
, pal.tree.
Tree
)
pal.substmodel.
RateMatrix
(also extends java.lang.Cloneable, pal.misc.
NamedParameterized
, pal.misc.
Report
)
pal.substmodel.
RateMatrixGroup
pal.algorithmics.
StoppingCriteria
pal.algorithmics.
StoppingCriteria.Factory
pal.substmodel.
SubstitutionModel
(also extends pal.misc.
Parameterized
, pal.misc.
Report
)
pal.misc.
Summarizable
pal.substmodel.
TemporalModelChange
pal.tree.
Tree
(also extends pal.misc.
IdGroup
, pal.misc.
Units
, pal.misc.
UnitsProvider
)
pal.tree.
ParameterizedTree
(also extends pal.misc.
Parameterized
)
pal.eval.
UnconstrainedLikelihoodModel.External
pal.eval.
UnconstrainedLikelihoodModel.Instance
pal.eval.
SiteDetails
pal.algorithmics.
StateProvider
pal.supgma.
SUPGMABase.CISummary
pal.supgma.
SUPGMABase.PopulationParameters
pal.misc.
TableReport
pal.alignment.
CharacterAlignment
(also extends pal.misc.
IdGroup
, pal.misc.
Report
, java.io.Serializable)
pal.supgma.
ThetaHandler
pal.statistics.
TopologyTestEngine.StatisticsHandler
pal.statistics.
TopologyTestEngine.TestResult
pal.statistics.
TopologyTestEngine.TopologyPool
pal.datatype.
TransitionPenaltyTable
pal.tree.
TreeGenerator
pal.tree.
TreeIterator
pal.tree.
TreeManipulator.BranchAccess
pal.tree.
TreeOperation
pal.eval.
UnconstrainedLikelihoodModel
pal.eval.
UnconstrainedLikelihoodModel.Internal
pal.eval.
UnconstrainedLikelihoodModel.Leaf
pal.algorithmics.
UndoableAction
pal.misc.
Units
pal.tree.
ParameterizedTree
(also extends pal.misc.
Parameterized
, pal.tree.
Tree
)
pal.tree.
Tree
(also extends pal.misc.
IdGroup
, java.io.Serializable, pal.misc.
UnitsProvider
)
pal.tree.
ParameterizedTree
(also extends pal.misc.
Parameterized
)
pal.misc.
UnitsProvider
pal.tree.
ParameterizedTree
(also extends pal.misc.
Parameterized
, pal.tree.
Tree
)
pal.tree.
Tree
(also extends pal.misc.
IdGroup
, java.io.Serializable, pal.misc.
Units
)
pal.tree.
ParameterizedTree
(also extends pal.misc.
Parameterized
)
pal.math.
UnivariateFunction
pal.tree.
UnrootedTreeInterface
pal.tree.
UnrootedTreeInterface.GeneralBranch
pal.tree.
UnrootedTreeInterface.BaseBranch
pal.tree.
UnrootedTreeInterface.UBranch
pal.tree.
UnrootedTreeInterface.Instructee
pal.tree.
UnrootedTreeInterface.UNode
pal.util.
XMLConstants
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV
NEXT
FRAMES
NO FRAMES
All Classes