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Package Hierarchies:
jebl.evolution.align
,
jebl.evolution.align.scores
,
jebl.evolution.aligners
,
jebl.evolution.alignments
,
jebl.evolution.characters
,
jebl.evolution.coalescent
,
jebl.evolution.distances
,
jebl.evolution.graphs
,
jebl.evolution.io
,
jebl.evolution.parsimony
,
jebl.evolution.sequences
,
jebl.evolution.substmodel
,
jebl.evolution.taxa
,
jebl.evolution.treemetrics
,
jebl.evolution.trees
,
jebl.evolution.treesimulation
,
jebl.math
,
jebl.util
Class Hierarchy
java.lang.Object
jebl.evolution.substmodel.
AbstractRateMatrix
(implements jebl.evolution.substmodel.
RateMatrix
)
jebl.evolution.substmodel.
AminoAcidModel
jebl.evolution.substmodel.
WAG
jebl.evolution.align.
Align
jebl.evolution.align.
MaximalSegmentPair
jebl.evolution.align.
NeedlemanWunsch
jebl.evolution.align.
NeedlemanWunschAffine
jebl.evolution.align.
NeedlemanWunschLinearSpace
jebl.evolution.align.
NeedlemanWunschLinearSpaceAffine
(implements jebl.evolution.align.
PairwiseAligner
)
jebl.evolution.align.
NonOverlapMultipleLocalAffine
jebl.evolution.align.
OldNeedlemanWunschAffine
jebl.evolution.align.
OverlapAlign
jebl.evolution.align.
SmithWaterman
jebl.evolution.align.
SmithWatermanLinearSpace
jebl.evolution.align.
SmithWatermanLinearSpaceAffine
jebl.evolution.align.
AlignCommand
jebl.evolution.align.
AlignmentTreeBuilderFactory
jebl.evolution.align.
AlignmentTreeBuilderFactory.Result
jebl.evolution.sequences.
AminoAcids
jebl.util.
Attributable.Utils
jebl.util.
AttributableHelper
(implements jebl.util.
Attributable
)
jebl.evolution.align.
BartonSternberg
(implements jebl.evolution.align.
MultipleAligner
)
jebl.evolution.trees.
BaseEdge
(implements jebl.evolution.graphs.
Edge
)
jebl.evolution.trees.
BaseNode
(implements jebl.evolution.graphs.
Node
)
jebl.evolution.alignments.
BasicAlignment
(implements jebl.evolution.alignments.
Alignment
)
jebl.evolution.distances.
BasicDistanceMatrix
(implements jebl.evolution.distances.
DistanceMatrix
)
jebl.evolution.distances.
F84DistanceMatrix
jebl.evolution.distances.
HKYDistanceMatrix
jebl.evolution.distances.
JukesCantorDistanceMatrix
jebl.evolution.align.
SequenceAlignmentsDistanceMatrix
jebl.evolution.distances.
TamuraNeiDistanceMatrix
jebl.evolution.sequences.
BasicSequence
(implements jebl.evolution.sequences.
Sequence
)
jebl.evolution.treemetrics.
BilleraMetric
(implements jebl.evolution.treemetrics.
RootedTreeMetric
)
jebl.math.
Binomial
jebl.evolution.io.
ByteBuilder
(implements java.lang.Appendable, java.lang.CharSequence)
jebl.evolution.trees.
CalculateSplitRates
jebl.evolution.sequences.
CanonicalSequence
(implements jebl.evolution.sequences.
Sequence
)
jebl.evolution.treemetrics.
CladeHeightMetric
(implements jebl.evolution.treemetrics.
RootedTreeMetric
)
jebl.evolution.trees.
CladeSystem
jebl.evolution.trees.
AttributedCladeSystem
jebl.evolution.trees.
ClusteringTreeBuilder
<T> (implements jebl.evolution.trees.
TreeBuilder
<T>)
jebl.evolution.trees.
NeighborJoiningTreeBuilder
jebl.evolution.coalescent.
Coalescent
(implements jebl.math.
MultivariateFunction
)
jebl.evolution.treesimulation.
CoalescentIntervalGenerator
(implements jebl.evolution.treesimulation.
IntervalGenerator
)
jebl.evolution.sequences.
Codons
jebl.evolution.trees.
CompactRootedTree
(implements jebl.evolution.trees.
RootedTree
)
jebl.evolution.alignments.
ConsensusSequence
(implements jebl.evolution.sequences.
Sequence
)
jebl.evolution.trees.
ConsensusTreeBuilder
<T> (implements jebl.evolution.trees.
TreeBuilder
<T>)
jebl.evolution.coalescent.
ConstantPopulation
(implements jebl.evolution.coalescent.
DemographicFunction
)
jebl.evolution.coalescent.
ExponentialGrowth
jebl.evolution.coalescent.
CataclysmicDemographic
jebl.evolution.coalescent.
ConstExponential
jebl.evolution.coalescent.
Expansion
jebl.evolution.coalescent.
LogisticGrowth
jebl.evolution.coalescent.
ConstLogistic
jebl.evolution.coalescent.
ExponentialLogistic
jebl.evolution.characters.
ContinuousCharacter
(implements jebl.evolution.characters.
Character
)
jebl.evolution.coalescent.
DemographicFunction.Utils
jebl.evolution.characters.
DiscreteCharacter
(implements jebl.evolution.characters.
Character
)
jebl.evolution.coalescent.
EmpiricalDemographicFunction
(implements jebl.evolution.coalescent.
DemographicFunction
)
jebl.evolution.io.
FastaExporter
(implements jebl.evolution.io.
SequenceExporter
)
jebl.evolution.io.
FastaImporter
(implements jebl.evolution.io.
ImmediateSequenceImporter
, jebl.evolution.io.
SequenceImporter
)
jebl.evolution.trees.
FilteredRootedTree
(implements jebl.evolution.trees.
RootedTree
)
jebl.evolution.trees.
ReRootedTree
jebl.evolution.trees.
SortedRootedTree
jebl.evolution.trees.
TransformedRootedTree
jebl.evolution.sequences.
FilteredSequence
(implements jebl.evolution.sequences.
Sequence
)
jebl.evolution.sequences.
GaplessSequence
jebl.evolution.sequences.
TranslatedSequence
jebl.evolution.parsimony.
FitchParsimony
(implements jebl.evolution.parsimony.
ParsimonyCriterion
)
jebl.util.
FixedBitSet
jebl.math.
GammaFunction
jebl.evolution.sequences.
GeneticCode
jebl.evolution.graphs.
Graph.Utils
jebl.util.
HashPair
<T>
jebl.evolution.io.
ImportHelper
jebl.evolution.coalescent.
IntervalList.Utils
jebl.evolution.coalescent.
Intervals
(implements jebl.evolution.coalescent.
IntervalList
)
jebl.math.
MachineAccuracy
jebl.math.
MatrixCalc
jebl.evolution.substmodel.
MatrixExponential
(implements java.lang.Cloneable, java.io.Serializable)
jebl.evolution.io.
MEGAExporter
(implements jebl.evolution.io.
AlignmentExporter
)
jebl.math.
MinimiserMonitor.Utils
jebl.evolution.distances.
ModelBasedDistanceMatrix
jebl.evolution.trees.
MostProbableTopology
jebl.math.
MultivariateMinimum
jebl.math.
OrthogonalSearch
jebl.evolution.trees.
MutableRootedTree
(implements jebl.evolution.trees.
RootedTree
)
jebl.evolution.io.
NewickExporter
(implements jebl.evolution.io.
TreeExporter
)
jebl.evolution.io.
NewickImporter
(implements jebl.evolution.io.
TreeImporter
)
jebl.evolution.io.
NexusExporter
(implements jebl.evolution.io.
AlignmentExporter
, jebl.evolution.io.
SequenceExporter
, jebl.evolution.io.
TreeExporter
)
jebl.evolution.io.
NexusImporter
(implements jebl.evolution.io.
AlignmentImporter
, jebl.evolution.io.
DistanceMatrixImporter
, jebl.evolution.io.
SequenceImporter
, jebl.evolution.io.
TreeImporter
)
jebl.evolution.sequences.
Nucleotides
jebl.util.
NumberFormatter
jebl.math.
NumericalDerivative
jebl.math.
OrderEnumerator.Utils
jebl.math.
OrthogonalHints.Utils
jebl.math.
OrthogonalLineFunction
(implements jebl.math.
UnivariateFunction
)
jebl.evolution.align.
Output
jebl.evolution.align.
PairwiseAligner.Result
jebl.evolution.io.
PHYLIPExporter
(implements jebl.evolution.io.
AlignmentExporter
, jebl.evolution.io.
TreeExporter
)
jebl.evolution.io.
PhylipSequentialImporter
(implements jebl.evolution.io.
SequenceImporter
)
jebl.evolution.align.
ProfileCharacter
jebl.util.
ProgressListener
(implements jebl.util.
Cancelable
)
jebl.util.
BasicProgressListener
jebl.util.
CompositeProgressListener
jebl.util.
ProgressListener.Wrapper
jebl.math.
Random
jebl.evolution.alignments.
ResampledAlignment
(implements jebl.evolution.alignments.
Alignment
)
jebl.evolution.alignments.
BootstrappedAlignment
jebl.evolution.alignments.
JackknifedAlignment
jebl.evolution.treemetrics.
RobinsonsFouldMetric
(implements jebl.evolution.treemetrics.
RootedTreeMetric
)
jebl.evolution.trees.
RootedFromUnrooted
(implements jebl.evolution.trees.
RootedTree
)
jebl.evolution.trees.
RootedSubtree
(implements jebl.evolution.trees.
RootedTree
)
jebl.evolution.trees.
RootedTreeUtils
jebl.evolution.align.scores.
Scores
(implements jebl.evolution.align.scores.
ScoreMatrix
)
jebl.evolution.align.scores.
AminoAcidScores
jebl.evolution.align.scores.
Blosum45
jebl.evolution.align.scores.
Blosum50
jebl.evolution.align.scores.
Blosum55
jebl.evolution.align.scores.
Blosum60
jebl.evolution.align.scores.
Blosum62
jebl.evolution.align.scores.
Blosum65
jebl.evolution.align.scores.
Blosum70
jebl.evolution.align.scores.
Blosum75
jebl.evolution.align.scores.
Blosum80
jebl.evolution.align.scores.
Blosum85
jebl.evolution.align.scores.
Blosum90
jebl.evolution.align.scores.
Pam100
jebl.evolution.align.scores.
Pam110
jebl.evolution.align.scores.
Pam120
jebl.evolution.align.scores.
Pam130
jebl.evolution.align.scores.
Pam140
jebl.evolution.align.scores.
Pam150
jebl.evolution.align.scores.
Pam160
jebl.evolution.align.scores.
Pam170
jebl.evolution.align.scores.
Pam180
jebl.evolution.align.scores.
Pam190
jebl.evolution.align.scores.
Pam200
jebl.evolution.align.scores.
Pam210
jebl.evolution.align.scores.
Pam220
jebl.evolution.align.scores.
Pam230
jebl.evolution.align.scores.
Pam240
jebl.evolution.align.scores.
Pam250
jebl.evolution.align.scores.
NucleotideScores
jebl.evolution.align.scores.
Hamming
jebl.evolution.align.scores.
JukesCantor
jebl.evolution.align.scores.
SubstScoreMatrix
jebl.evolution.align.scores.
ScoresFactory
jebl.evolution.align.
SequenceShuffler
jebl.evolution.sequences.
SequenceTester
jebl.evolution.sequences.
SequenceType.Utils
jebl.evolution.trees.
SimpleRootedTree
(implements jebl.evolution.trees.
RootedTree
)
jebl.evolution.trees.
SimpleTree
(implements jebl.evolution.trees.
Tree
)
jebl.evolution.trees.
SplitSystem
jebl.evolution.trees.
SplitUtils
jebl.evolution.sequences.
State
(implements java.lang.Comparable<T>)
jebl.evolution.sequences.
AminoAcidState
jebl.evolution.sequences.
CodonState
jebl.evolution.sequences.
NucleotideState
jebl.evolution.sequences.
StateClassification.Default
(implements jebl.evolution.sequences.
StateClassification
)
jebl.evolution.io.
TabDelimitedImporter
(implements jebl.evolution.io.
DistanceMatrixImporter
)
jebl.evolution.taxa.
Taxon
(implements jebl.util.
Attributable
, java.lang.Comparable<T>)
jebl.evolution.taxa.
TaxonomicLevel
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
jebl.evolution.graphs.
Graph.NoEdgeException
jebl.evolution.io.
ImportException
jebl.evolution.io.
ImportException.BadFormatException
jebl.evolution.io.
ImportException.DuplicateFieldException
jebl.evolution.io.
ImportException.DuplicateTaxaException
jebl.evolution.io.
ImportException.MissingFieldException
jebl.evolution.io.
ImportException.ShortSequenceException
jebl.evolution.io.
ImportException.TooFewTaxaException
jebl.evolution.io.
ImportException.UnknownTaxonException
jebl.evolution.io.
ImportException.UnparsableDataException
jebl.evolution.io.
NexusImporter.MissingBlockException
jebl.math.
MatrixCalcException
jebl.math.
MatrixCalcException.NotSquareMatrixException
jebl.math.
MatrixCalcException.PositiveDefiniteException
java.lang.RuntimeException
java.lang.IllegalArgumentException
jebl.evolution.distances.
CannotBuildDistanceMatrixException
jebl.evolution.sequences.
SequenceStateException
jebl.evolution.taxa.
MissingTaxonException
jebl.evolution.align.
Traceback
jebl.evolution.trees.
TreeBiPartitionInfo
jebl.evolution.trees.
TreeBuilderFactory
jebl.evolution.trees.
TreeChangeEvent
jebl.evolution.trees.
TreeChangeListener
jebl.evolution.trees.
TreeSelectionChangeEvent
jebl.evolution.treesimulation.
TreeSimulator
jebl.math.
UnivariateMinimum
jebl.evolution.graphs.
Utils
jebl.evolution.sequences.
Utils
jebl.evolution.trees.
Utils
jebl.util.
Utils
Interface Hierarchy
jebl.evolution.aligners.
Aligner
jebl.evolution.io.
AlignmentExporter
jebl.evolution.io.
AlignmentImporter
jebl.util.
Attributable
jebl.evolution.graphs.
Edge
jebl.evolution.graphs.
Graph
jebl.evolution.trees.
RootedTree
jebl.evolution.trees.
Tree
jebl.evolution.trees.
RootedTree
jebl.evolution.graphs.
Node
jebl.evolution.trees.
RootedTree
jebl.evolution.sequences.
Sequence
(also extends java.lang.Comparable<T>)
jebl.evolution.trees.
Tree
jebl.evolution.trees.
RootedTree
jebl.util.
Cancelable
jebl.evolution.characters.
Character
jebl.evolution.characters.
CharacterType
java.lang.Cloneable
jebl.evolution.substmodel.
RateMatrix
(also extends java.io.Serializable)
java.lang.Comparable<T>
jebl.evolution.sequences.
Sequence
(also extends jebl.util.
Attributable
)
jebl.evolution.coalescent.
DemographicFunction
jebl.evolution.distances.
DistanceMatrix
jebl.evolution.io.
DistanceMatrixImporter
jebl.evolution.io.
ImmediateSequenceImporter
jebl.evolution.io.
ImmediateSequenceImporter.Callback
jebl.evolution.treesimulation.
IntervalGenerator
jebl.evolution.coalescent.
IntervalList
java.lang.Iterable<T>
jebl.evolution.io.
TreeImporter
jebl.math.
MinimiserMonitor
jebl.evolution.align.
MultipleAligner
jebl.math.
MultivariateFunction
jebl.math.
MultivariateMinimum.Factory
jebl.math.
OrderEnumerator
jebl.math.
OrderEnumerator.OEFactory
jebl.math.
OrthogonalHints
jebl.evolution.align.
PairwiseAligner
jebl.evolution.parsimony.
ParsimonyCriterion
jebl.evolution.alignments.
Pattern
jebl.evolution.alignments.
Patterns
jebl.evolution.alignments.
Alignment
(also extends jebl.evolution.sequences.
Sequences
)
jebl.evolution.treemetrics.
RootedTreeMetric
jebl.evolution.align.scores.
ScoreMatrix
jebl.evolution.io.
SequenceExporter
jebl.evolution.io.
SequenceImporter
jebl.evolution.sequences.
Sequences
jebl.evolution.alignments.
Alignment
(also extends jebl.evolution.alignments.
Patterns
)
jebl.evolution.sequences.
SequenceType
java.io.Serializable
jebl.evolution.substmodel.
RateMatrix
(also extends java.lang.Cloneable)
jebl.util.
SimpleListener
jebl.evolution.sequences.
StateClassification
jebl.evolution.align.
TracebackPlotter
jebl.evolution.trees.
TreeBuilder
<T>
jebl.evolution.io.
TreeExporter
jebl.math.
UnivariateFunction
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
jebl.evolution.coalescent.
IntervalList.IntervalType
jebl.evolution.io.
IllegalCharacterPolicy
jebl.evolution.io.
NexusImporter.NexusBlock
jebl.evolution.io.
DistanceMatrixImporter.Triangle
jebl.evolution.trees.
ConsensusTreeBuilder.Method
jebl.evolution.trees.
ReRootedTree.RootingType
jebl.evolution.trees.
TransformedRootedTree.Transform
jebl.evolution.trees.
SortedRootedTree.BranchOrdering
jebl.evolution.trees.
TreeBuilderFactory.Method
jebl.evolution.trees.
TreeBuilderFactory.DistanceModel
jebl.evolution.trees.
TreeBuilderFactory.ConsensusMethod
jebl.evolution.trees.
TreeBiPartitionInfo.DistanceNorm
jebl.util.
MaybeBoolean
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV NEXT
FRAMES
NO FRAMES
All Classes
http://code.google.com/p/jebl2/