- AbstractNode
- BoxPlotUtils
- ClassificationParser
- ClassificationResult
- ClassificationResultFormatter
- ClassificationResultFormatter.FORMAT
- Classifier
- ClassifierCmd
- ClassifierFactory
- ClassifierGridware
- ClassifierMain
- ClassifierSequence
- ClassifierTraineeMaker
- ClassifierTreeBuilder
- ClassifierTreeBuilder.ClassifierTaxonFactory
- CmdOptions
- CompareMisclassified
- CompareTrainingSets
- ComparisonBrowserBean
- ComparisonBrowserNode
- ComparisonCmd
- ComparisonResultTreeSet
- ComparisonResultTreeSet.ComparisonResultComparator
- CopyNumberParser
- CorrectAssignment
- CrossValidate
- CrossValidateMain
- DecisionMaker
- DefaultPrintVisitor
- EstimateSPrintVisitor
- FindWindowFrame
- GenusWordConditionalProb
- GenusWordProbFileParser
- HierarchyTree
- HierarchyTree
- HierarchyVersion
- LeaveOneOutTester
- LeaveOneOutTesterMain
- LineageSequence
- LineageSequenceParser
- LogWordPriorFileParser
- Main
- MainMovingWindow
- MCSample
- MCSamplePrintUtil
- MCSampleResult
- MCTaxon
- MergeTaxonCount
- MultiClassifier
- MultiClassifierResult
- NameRankDupException
- NBClassifier
- PairwiseSeqDistance
- PixelCalculatorBean
- ProbIndexFileParser
- RankAssignment
- RawGenusWordConditionalProb
- RawHierarchyTree
- RdmSelectTaxon
- Reprocess
- Score
- SeqErrorBean
- SeqInfo
- ShortSequenceException
- SigCalculator
- SortedROCSet
- SortedROCSet.PredictionCount
- SortedROCSet.ResultComparator
- StatusCount
- StatusCountUtils
- TaxaSimilarityMain
- Taxon
- Taxonomy
- Taxonomy
- TaxonTree
- TrainingDataException
- TrainingInfo
- TreeFactory
- TreeFactory
- TreeFileParser
- UncNode
- Unifrac
- UnifracTaxon
- UnifracTree
- UnifracTree.UnifracResult
- UnifracTreeBuilder
- UnifracTreeBuilder.UnifracSample
- ValidationClassificationResult
- ValidClassificationResultFacade
- Window
- WindowTester
- Ztable