All Classes

  • AbstractRateMatrix
  • AbstractRootedTree
  • Align
  • AlignCommand
  • Aligner
  • Alignment
  • AlignmentExporter
  • AlignmentImporter
  • AlignmentTreeBuilderFactory
  • AlignmentTreeBuilderFactory.Result
  • AminoAcidModel
  • AminoAcids
  • AminoAcidScores
  • AminoAcidState
  • Attributable
  • Attributable.Utils
  • AttributableHelper
  • AttributedCladeSystem
  • BartonSternberg
  • BaseEdge
  • BaseNode
  • BasicAlignment
  • BasicDistanceMatrix
  • BasicProgressListener
  • BasicSequence
  • BilleraMetric
  • Binomial
  • Blosum45
  • Blosum50
  • Blosum55
  • Blosum60
  • Blosum62
  • Blosum65
  • Blosum70
  • Blosum75
  • Blosum80
  • Blosum85
  • Blosum90
  • BootstrappedAlignment
  • ByteBuilder
  • CalculateSplitRates
  • Cancelable
  • CannotBuildDistanceMatrixException
  • CanonicalSequence
  • CataclysmicDemographic
  • Character
  • CharacterType
  • CladeHeightMetric
  • CladeSystem
  • ClusteringTreeBuilder
  • Coalescent
  • CoalescentIntervalGenerator
  • Codons
  • CodonSequence
  • CodonState
  • CompactRootedTree
  • CompositeProgressListener
  • ConsensusSequence
  • ConsensusTreeBuilder
  • ConsensusTreeBuilder.Method
  • ConstantPopulation
  • ConstExponential
  • ConstLogistic
  • ContinuousCharacter
  • DemographicFunction
  • DemographicFunction.Utils
  • DiscreteCharacter
  • DistanceMatrix
  • DistanceMatrixImporter
  • DistanceMatrixImporter.Triangle
  • Edge
  • EmpiricalDemographicFunction
  • Expansion
  • ExponentialGrowth
  • ExponentialLogistic
  • F84DistanceMatrix
  • FastaExporter
  • FastaImporter
  • FilteredRootedTree
  • FilteredSequence
  • FitchParsimony
  • FixedBitSet
  • GammaFunction
  • GaplessSequence
  • GeneticCode
  • Graph
  • Graph.NoEdgeException
  • Graph.Utils
  • Hamming
  • HashPair
  • HKYDistanceMatrix
  • IllegalCharacterPolicy
  • ImmediateSequenceImporter
  • ImmediateSequenceImporter.Callback
  • ImportException
  • ImportException.BadFormatException
  • ImportException.DuplicateFieldException
  • ImportException.DuplicateTaxaException
  • ImportException.MissingFieldException
  • ImportException.ShortSequenceException
  • ImportException.TooFewTaxaException
  • ImportException.UnknownTaxonException
  • ImportException.UnparsableDataException
  • ImportHelper
  • IntervalGenerator
  • IntervalList
  • IntervalList.IntervalType
  • IntervalList.Utils
  • Intervals
  • JackknifedAlignment
  • JukesCantor
  • JukesCantorDistanceMatrix
  • LogisticGrowth
  • MachineAccuracy
  • MatrixCalc
  • MatrixCalcException
  • MatrixCalcException.NotSquareMatrixException
  • MatrixCalcException.PositiveDefiniteException
  • MatrixExponential
  • MaximalSegmentPair
  • MaybeBoolean
  • MEGAExporter
  • MinimiserMonitor
  • MinimiserMonitor.Utils
  • MissingTaxonException
  • ModelBasedDistanceMatrix
  • MostProbableTopology
  • MultipleAligner
  • MultivariateFunction
  • MultivariateMinimum
  • MultivariateMinimum.Factory
  • MutableRootedTree
  • NeedlemanWunsch
  • NeedlemanWunschAffine
  • NeedlemanWunschLinearSpace
  • NeedlemanWunschLinearSpaceAffine
  • NeighborJoiningTreeBuilder
  • NewickExporter
  • NewickImporter
  • NexusExporter
  • NexusImporter
  • NexusImporter.MissingBlockException
  • NexusImporter.NexusBlock
  • Node
  • NonOverlapMultipleLocalAffine
  • Nucleotides
  • NucleotideScores
  • NucleotideState
  • NumberFormatter
  • NumericalDerivative
  • OldNeedlemanWunschAffine
  • OrderEnumerator
  • OrderEnumerator.OEFactory
  • OrderEnumerator.Utils
  • OrthogonalHints
  • OrthogonalHints.Utils
  • OrthogonalLineFunction
  • OrthogonalSearch
  • Output
  • OverlapAlign
  • PairwiseAligner
  • PairwiseAligner.Result
  • Pam100
  • Pam110
  • Pam120
  • Pam130
  • Pam140
  • Pam150
  • Pam160
  • Pam170
  • Pam180
  • Pam190
  • Pam200
  • Pam210
  • Pam220
  • Pam230
  • Pam240
  • Pam250
  • ParsimonyCriterion
  • Pattern
  • Patterns
  • PHYLIPExporter
  • PhylipSequentialImporter
  • ProfileCharacter
  • ProgressListener
  • ProgressListener.Wrapper
  • Random
  • RateMatrix
  • ReRootedTree
  • ResampledAlignment
  • RobinsonsFouldMetric
  • RootedFromUnrooted
  • RootedSubtree
  • RootedTree
  • RootedTreeMetric
  • RootedTreeUtils
  • ScoreMatrix
  • Scores
  • ScoresFactory
  • Sequence
  • SequenceAlignmentsDistanceMatrix
  • SequenceExporter
  • SequenceImporter
  • Sequences
  • SequenceShuffler
  • SequenceStateException
  • SequenceTester
  • SequenceType
  • SequenceType.Utils
  • SimpleListener
  • SimpleRootedTree
  • SimpleTree
  • SmithWaterman
  • SmithWatermanLinearSpace
  • SmithWatermanLinearSpaceAffine
  • SortedRootedTree
  • SortedRootedTree.BranchOrdering
  • SplitSystem
  • SplitUtils
  • State
  • StateClassification
  • StateClassification.Default
  • SubstScoreMatrix
  • SystemOut
  • TabDelimitedImporter
  • TamuraNeiDistanceMatrix
  • Taxon
  • TaxonomicLevel
  • Traceback
  • TracebackPlotter
  • TransformedRootedTree
  • TransformedRootedTree.Transform
  • TranslatedSequence
  • Tree
  • TreeBiPartitionInfo
  • TreeBiPartitionInfo.DistanceNorm
  • TreeBuilder
  • TreeBuilderFactory
  • TreeBuilderFactory.ConsensusMethod
  • TreeBuilderFactory.DistanceModel
  • TreeBuilderFactory.Method
  • TreeChangeEvent
  • TreeChangeListener
  • TreeExporter
  • TreeImporter
  • TreeSelectionChangeEvent
  • TreeSimulator
  • UnivariateFunction
  • UnivariateMinimum
  • Utils
  • Utils
  • Utils
  • Utils
  • WAG