All Classes
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