- App
- BlastHomologyHits
- BlastXMLQuery
- ChromosomeMappingTools
- ChromPos
- Cytoband
- CytobandParser
- Fastq
- FastqBuilder
- FastqReader
- FastqTools
- FastqVariant
- FastqWriter
- Feature
- FeatureHelper
- FeatureI
- FeatureList
- GCStats
- GeneChromosomePosition
- GeneChromosomePositionParser
- GeneFeatureHelper
- GeneIDGFF2Reader
- GeneIDXMLReader
- GeneMarkGTFReader
- GeneName
- GeneNamesParser
- GFF3FromUniprotBlastHits
- GFF3Reader
- GFF3Writer
- IlluminaFastqReader
- IlluminaFastqWriter
- Location
- LocIterator
- OutputHitsGFF
- ParseListener
- ProteinMappingTools
- SangerFastqReader
- SangerFastqWriter
- SimpleTwoBitFileProvider
- SolexaFastqReader
- SolexaFastqWriter
- SplitFasta
- StainType
- StreamListener
- TwoBitFacade
- TwoBitParser
- UniprotToFasta