AlignmentInterologScorer
AlignmentInterologScorer.AlignmentScoring
Arc
BlastBBHAlignmentLengthConstraint
BlastBBHConstraints
BlastHit
BlastHitFileParser
BlastHits
BooleanExpression
Bootstrap
BootstrapClustering
BootstrapClusterings
BroheeSimilarity
ChartTools
Clusterer
Colocalization
CombinationRules
CombinationRules.CombinationType
CombinationRules.WeightMergePolicy
CommonAncestors
Complex
ComplexEnrichment
ComplexMapping
ComplexMappings
ComplexScoreCalculator
ComplexSet
ComplexSetComparison
ComplexSetReader
ComplexSetWriter
CorrelationCoefficient
DiceCoefficients
DummyClusterer
DummyClusterer
DummyScores
EvalueInterologScorer
FASTAParser
FunctionalSimilarities
FunctionalSimilaritiesSchlicker
FunctionalSimilaritiesSchlicker.FunctionalSimilarityMeasure
GOAnnotationReader
GOAnnotations
GONetwork
GONetwork.Namespace
GONetwork.Relationships
GOTerm
HartCalculator
HierarchicalClusterer
HierarchicalClusteringTrees
HierarchicalLinkage
HierarchicalTreeNode
HypergeometricDistribution
InterologsCalculator
InterologScorer
InvalidExpressionException
LocalizationData
LocalizationDataReader
MarkovClusterer
MCLEfficiencyCalculator
MCLParameters
MTRandom
NetworkComparison
NetworkEdge
NetworkGenerator
NetworkReader
NetworkSearchCallback
NetworkWriter
PearsonCoefficient
PECalculator
PetriNetCreator
Place
Point
ProCopeException
ProteinManager
ProteinNetwork
ProteinSet
ProtManager
PurificationBootstrapSamples
PurificationData
PurificationDataReader
PurificationDataWriter
PurificationExperiment
ROC
ROCCurve
ROCCurveHandler
ROCPoint
ScoresCalculator
SequenceAligner
Sequences
SocioAffinityCalculator
SparseMatrixInt
SpearmanCoefficient
StringToIntMapper
Synonyms
TermSimilarities
TermSimilaritiesSchlicker
TermSimilaritiesSchlicker.TermSimilarityMeasure
Tools
ToPNetGenerator
Transition
UseCase1
UseCase2
UseCase3
UseCase4
UserClassSpecException
UserClusterer
UserDataType
UserParameter
UserScoresCalculator
XGMMLGenerator
XGMMLWriter
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