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ActivityCharEncodingTable
ActivityColorListener
ActivityNotFoundException
Alignment
Alignment.RulerAnnotation
AlignmentAlgorithm
AlignmentAlgorithmConfigurationStep
AlignmentFrame
AlignmentListener
AlignmentNamePanel
AlignmentPanel
AlignmentSorter
AlignmentTree
AlignmentTreeNode
AlignmentTreeVisualization
AlignmentType
ArrayMatrixFileIO
ColorEditor
ColorRenderer
ColorSequenceDialog
ColumnFilter
ColumnFilterComponent
ColumnFilterDialog
ColumnSort
ColumnSortComponent
ColumnSortDialog
ConsensusComponent
ConsensusSequence
DisplayProperties
DisplayPropertiesListener
EditActivityAnnotationDialog
EditSeqAnnBaseDialog
EditSequenceDialog
EditSequenceNameDialog
FileIO
FixedWidthTextField
GuideTreeAlignment
IndelSubstitutionScore
IntroductionStep
JListX
LazyBoundedRangeModel
MineAlignment
MSA
myStep
RealignmentConfigurationStep
RealignmentStrategy
RefineAlignment
RulerAnnotationComponent
RulerComponent
ScoringMatricesConfigurationStep
ScoringMatrix
ScrollableGridLayout
ScrollableViewport
SeqAlignment
SeqAlignment.TraceBack
Sequence
SequenceAlignment
SequenceAlignmentLeftIndel
SequenceComponent
SequenceListener
SequenceNameComponent
Temp
TraceAlignmentWithGuideTreeInput
TraceAlignmentWithGuideTreePlugin
TraceAlignmentWithGuideTreeSettingsListener
TraceAlignmentWithGuideTreeUI
TraceBack
UkkonenSuffixTree
Utils
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