Hierarchy For All Packages
- 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.substmodel.AminoAcidModel
- jebl.evolution.trees.AbstractRootedTree (implements jebl.evolution.trees.RootedTree)
- jebl.evolution.trees.FilteredRootedTree
- jebl.evolution.trees.SortedRootedTree
- jebl.evolution.trees.TransformedRootedTree
- jebl.evolution.trees.MutableRootedTree
- jebl.evolution.trees.ReRootedTree
- jebl.evolution.trees.RootedFromUnrooted
- jebl.evolution.trees.RootedSubtree
- jebl.evolution.trees.FilteredRootedTree
- 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.sequences.CodonSequence (implements jebl.evolution.sequences.Sequence)
- 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.coalescent.ExponentialGrowth
- 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.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.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.SystemOut
- 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.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.AminoAcidScores
- 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
- java.lang.RuntimeException
- java.lang.IllegalArgumentException
- jebl.evolution.distances.CannotBuildDistanceMatrixException
- java.lang.IllegalArgumentException
- jebl.evolution.sequences.SequenceStateException
- jebl.evolution.taxa.MissingTaxonException
- java.lang.Exception
- 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
- jebl.evolution.substmodel.AbstractRateMatrix (implements jebl.evolution.substmodel.RateMatrix)
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.Tree
- jebl.evolution.trees.RootedTree
- jebl.evolution.trees.Tree
- jebl.evolution.graphs.Node
- jebl.evolution.sequences.Sequence (also extends java.lang.Comparable<T>)
- 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.treemetrics.RootedTreeMetric
- jebl.evolution.align.scores.ScoreMatrix
- jebl.evolution.io.SequenceExporter
- jebl.evolution.io.SequenceImporter
- jebl.evolution.sequences.Sequences
- 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 Class Hierarchy
- java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
- jebl.evolution.trees.ConsensusTreeBuilder.Method
- jebl.evolution.io.DistanceMatrixImporter.Triangle
- jebl.evolution.io.IllegalCharacterPolicy
- jebl.evolution.coalescent.IntervalList.IntervalType
- jebl.util.MaybeBoolean
- jebl.evolution.io.NexusImporter.NexusBlock
- jebl.evolution.trees.SortedRootedTree.BranchOrdering
- jebl.evolution.trees.TransformedRootedTree.Transform
- jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
- jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
- jebl.evolution.trees.TreeBuilderFactory.DistanceModel
- jebl.evolution.trees.TreeBuilderFactory.Method
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)