- AAindexFactory
- AAIndexFileParser
- AAIndexProvider
- ABITrace
- ABITracerCompoundSet
- AbstractCompound
- AbstractCompoundSet
- AbstractCompoundTranslator
- AbstractFeature
- AbstractLocation
- AbstractNucleotideCompoundSet
- AbstractReference
- AbstractSequence
- AbstractSequence.AnnotationType
- AccesionedLocation
- Accessioned
- AccessionID
- AlignedSequence
- AlignedSequence.Step
- AmbiguityDNACompoundSet
- AmbiguityDNARNAHybridCompoundSet
- AmbiguityRNACompoundSet
- AminoAcidCompound
- AminoAcidCompoundSet
- ArrayListProxySequenceReader
- ArrayListSequenceReader
- BasicSequence
- BitSequenceReader
- BitSequenceReader.BitArrayWorker
- BlastHitBuilder
- BlastHspBuilder
- BlastResult
- BlastResultBuilder
- BlastTabularParser
- BlastXMLParser
- BufferedReaderBytesRead
- CaseInsensitiveCompound
- CasePreservingProteinSequenceCreator
- CDSComparator
- CDSSequence
- ChromosomeSequence
- ClasspathResource
- CodonCompound
- ComplementCompound
- ComplementSequenceView
- Compound
- CompoundNotFoundException
- CompoundSet
- CompoundTranslator
- ConcurrencyTools
- CRC64Checksum
- DatabaseReferenceInterface
- DataSource
- DBReferenceInfo
- DefaultAAIndexProvider
- DemoSixFrameTranslation
- DNACompoundSet
- DNASequence
- DNASequence.DNAType
- DNASequenceCreator
- DNAToRNATranslator
- Edit
- Edit.AbstractEdit
- Edit.Delete
- Edit.Insert
- Edit.Substitute
- EmblId
- EmblReader
- EmblRecord
- EmblReference
- Equals
- ExonComparator
- ExonSequence
- FastaGeneWriter
- FastaHeaderFormatInterface
- FastaReader
- FastaReaderHelper
- FastaSequenceParser
- FastaWriter
- FastaWriterHelper
- FeatureDbReferenceInfo
- FeatureInterface
- FeatureRetriever
- FeaturesKeyWordInterface
- FileDownloadUtils
- FileDownloadUtils.Hash
- FileProxyDNASequenceCreator
- FileProxyProteinSequenceCreator
- FileProxyRNASequenceCreator
- FlatFileCache
- FourBitSequenceReader
- FourBitSequenceReader.FourBitArrayWorker
- Frame
- FuzzyPoint
- GenbankHeaderFormatInterface
- GenbankProxySequenceReader
- GenbankReader
- GenbankReaderHelper
- GenbankReference
- GenbankSequenceParser
- GenbankWriter
- GenbankWriterHelper
- GenericFastaHeaderFormat
- GenericFastaHeaderParser
- GenericGenbankHeaderFormat
- GenericGenbankHeaderParser
- GenericInsdcHeaderFormat
- GeneSequence
- Hashcoder
- Hit
- Hsp
- InputStreamProvider
- InsdcLocations
- InsdcLocations.BondLocation
- InsdcLocations.GroupLocation
- InsdcLocations.OneOfLocation
- InsdcLocations.OrderLocation
- InsdcParser
- IntronSequence
- IOUtils
- IOUtils.ReaderProcessor
- IUPACParser
- IUPACParser.IUPACTable
- JoiningSequenceReader
- LightweightProfile
- LightweightProfile.StringFormat
- Location
- Location.Tools
- LocationHelper
- Messages
- MultipleSequenceAlignment
- MutableAlignedSequence
- MutableProfile
- MutableProfilePair
- MutableSequencePair
- NucleotideCompound
- ParseFastaFileDemo
- ParserException
- PlainFastaHeaderParser
- Point
- Point.Resolver
- PrettyXMLWriter
- Profile
- Profile.StringFormat
- ProfilePair
- ProfileView
- ProteinSequence
- ProteinSequenceCreator
- ProxySequenceReader
- Qualifier
- QualityFeature
- QuantityFeature
- ReferenceInterface
- Result
- ResultFactory
- ReversedSequenceView
- RNACompoundSet
- RNASequence
- RNASequenceCreator
- RnaSequenceView
- RNAToAminoAcidTranslator
- ScaledSubstitutionMatrix
- SearchIO
- Sequence
- SequenceAsStringHelper
- SequenceComparator
- SequenceCreatorInterface
- SequenceFileProxyLoader
- SequenceHeaderParserInterface
- SequenceLocation
- SequenceMixin
- SequenceMixin.SequenceIterator
- SequenceOptimizationHints
- SequenceOptimizationHints.SequenceCollection
- SequenceOptimizationHints.SequenceUsage
- SequencePair
- SequenceParserInterface
- SequenceProxyView
- SequenceReader
- SequenceTools
- SequenceView
- SimpleAlignedSequence
- SimpleLocation
- SimplePoint
- SimpleProfile
- SimpleProfilePair
- SimpleSequencePair
- SimpleSubstitutionMatrix
- SingleCompoundSequenceReader
- SingleLinkageClusterer
- SoftHashMap
- StartCodonSequence
- StopCodonSequence
- Strand
- StringManipulationHelper
- StringProxySequenceReader
- SubstitutionMatrix
- SubstitutionMatrixHelper
- Table
- Table.CaseInsensitiveTriplet
- Table.Codon
- TaxonomyID
- TextFeature
- TranscriptionEngine
- TranscriptionEngine.Builder
- TranscriptSequence
- TranslationException
- TwoBitSequenceReader
- TwoBitSequenceReader.TwoBitArrayWorker
- UncompressFile
- UncompressInputStream
- UniprotProxySequenceReader
- WindowedSequence
- XMLHelper
- XMLWriter