Clustering
Computable
CutoffCalculator
CycleInMultiMotifExeption
DefaultCommunicator
Distance
DoubleMotif
EuclideanDistance
FastaReader
ForwardClustering
FoundMotifStruct
GreedyClustering
GUIOutputStream
GuiTools
ICommunicator
IOperator
IOTools
jPREdictor
LikelihoodMeasure
MainPanel
MainWindow
ManhattanDistance
MappedCharSequence
Markable
Marker
MathTools
MatrixAlignment
MatrixDistance
MatrixLikelihood
MatrixLoglikelihood
MatrixRelationMeasure
MatrixSimilarity
MinkowskiDistance
MissingCharSequenceException
MissingMotifException
Motif
MotifAlignment
MotifCheckTree
MotifDistanceTree
MotifEvolution
MotifEvolutionES
MotifEvolutionFull
MotifEvolutionRewardedSelection
MotifFilter
MotifList
MotifMaker
MotifNotCompleteException
MotifSearchAdapter
MotifSearcher
MotifSearchWithError
MotifSearchWithThreshold
MotifTree
MouseOverHintManager
MultiFileReader
MultiMotif
MultiMotifAlignment
MultiplyOutputStream
NewSequenceBlockException
NilOutputStream
NoMoreSequencesAvailableException
Operator
OptionFile
PSPMotif
PSSMotif
Queue
RawReader
RegularExpressionMotif
RelationalCalculation
RelationMeasure
ResetableReader
ResetNotSupportedException
ScoreBand
ScoredSequenceStruct
ScorePlotBrowser
ScoringFactory
Sequence
SequenceEnumeration
SequenceEnumerator
SequenceFilter
SequenceInformationBlock
SequenceMotif
SequenceReader
SequenceWindowScorer
SingleMotifAlignment
States
StatusBar
TextInsertDialog
VectorRelationMeasure
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