- AbstractRateMatrix
- 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
- ReRootedTree.RootingType
- 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