Documentation

Files

A

• AbstractMolecularSequence.php
• AbstractNucleicSequence.php
• Accession.php
• AlignmentInputGuard.php
• AlternateGeneticCodeTranslator.php
• AlternateGeneticCodeTranslatorInterface.php
• AmelayeBioPHPExtension.php
• AminoAcidSequence.php
• AminoApi.php
• AminoApiAdapter.php
• AminoDTO.php
• Author.php

B

• BedFeatureReader.php
• BedFeatureReaderInterface.php
• BedFeatureWriter.php
• BedFeatureWriterInterface.php
• BedImportResult.php
• Bioapi.php

C

• CaiResult.php
• ChaosGameRepresentationCalculator.php
• ChaosGameRepresentationInterface.php
• CircularDnaSequence.php
• CircularRestrictionDigestManager.php
• CodonAdaptationIndexCalculator.php
• CodonAdaptationIndexInterface.php
• CodonOptimizer.php
• CodonOptimizerInterface.php
• CodonUsageTable.php
• CodonUsageTableBuilder.php
• CodonUsageTableBuilderInterface.php
• Collection.php
• CollectionElement.php
• Configuration.php
• CpGIsland.php
• CpGIslandFinder.php
• CpGIslandFinderInterface.php

D

• DatabaseInterface.php
• DatabaseManager.php
• DatabaseParserFactory.php
• DatabaseReaderFactory.php
• DatabaseRecorderFactory.php
• DistanceMatrix.php
• DnaSequence.php

E

• ElementApi.php
• ElementApiAdapter.php
• ElementDTO.php
• EntrezReference.php
• EntrezReferenceInterface.php
• EntryReader.php
• Enzyme.php
• ExpasyDisease.php
• ExpasyDiseaseInterface.php

F

• FastaWriter.php
• FastaWriterInterface.php
• FastqImportResult.php
• FastqReader.php
• FastqReaderInterface.php
• FastqRecord.php
• FastqWriter.php
• FastqWriterInterface.php
• Feature.php
• FeatureOverlap.php
• FeatureOverlapInterface.php
• FeatureOverlapManager.php
• FeatureType.php
• FormatsTrait.php

G

• GbSequence.php
• GenbankImportResult.php
• GenbankPlasmidMapper.php
• GenbankPlasmidMapperInterface.php
• GenbankWriter.php
• GenbankWriterInterface.php
• GeneticCodeTable.php
• GeneticsFunctions.php
• GenomeReference.php
• GenomeReferenceInterface.php
• GffFeatureReader.php
• GffFeatureReaderInterface.php
• GffFeatureWriter.php
• GffFeatureWriterInterface.php
• GffImportResult.php
• GibsonAssemblyInterface.php
• GibsonAssemblyManager.php
• GibsonHomologyArms.php
• GibsonJunctionResult.php

I

• InvalidAlignmentInputException.php
• InvalidDistanceMatrixException.php
• InvalidFastqRecordException.php
• InvalidFeatureCoordinatesException.php
• InvalidNewickException.php
• InvalidPhylogeneticTreeException.php
• InvalidSequenceException.php
• InvalidVcfRecordException.php

K

• Keyword.php

L

• LinearRestrictionDigestInterface.php
• LinearRestrictionDigestManager.php
• LinearRestrictionDigestResult.php

M

• MathematicsFunctions.php
• MeltingTemperatureCalculator.php
• MeltingTemperatureInterface.php
• MolecularSequenceFactory.php
• MoleculeAwareScoringInterface.php

N

• NearestNeighborTmResult.php
• NeedlemanWunschAligner.php
• NeedlemanWunschAlignerInterface.php
• NeighborJoiningInterface.php
• NeighborJoiningTreeBuilder.php
• NewickReader.php
• NewickReaderInterface.php
• NucleotidApi.php
• NucleotidApiAdapter.php
• NucleotidDTO.php
• NucleotideAmbiguityScoring.php

O

• OligosInterface.php
• OligosManager.php
• OpenReadingFrame.php
• OrfFinder.php
• OrfFinderInterface.php

P

• PKApi.php
• PKApiAdapter.php
• PKDTO.php
• PairwiseAlignmentResult.php
• Pam250MatrixDigitApi.php
• Pam250MatrixDigitApiAdapter.php
• Pam250MatrixDigitDTO.php
• Pam250Scoring.php
• ParseAaindexManager.php
• ParseBlocksManager.php
• ParseDatabaseInterface.php
• ParseDbAbstractManager.php
• ParseEmblManager.php
• ParseEntrezManager.php
• ParseEpdManager.php
• ParseExpasyEnzymeManager.php
• ParseGenbankManager.php
• ParseGenomeManager.php
• ParseHgbaseManager.php
• ParseKeggAbstractManager.php
• ParseKeggCompoundManager.php
• ParseKeggEnzymeManager.php
• ParseKeggGenomeManager.php
• ParseKeggOrthologManager.php
• ParseKeggReactionManager.php
• ParseNcbiLitManager.php
• ParsePdbManager.php
• ParsePdbstrManager.php
• ParsePirManager.php
• ParsePmdManager.php
• ParsePrfManager.php
• ParsePrintsManager.php
• ParseProdomManager.php
• ParsePrositeManager.php
• ParseSwissprotManager.php
• ParseTransfacAbstractManager.php
• ParseTransfacCellManager.php
• ParseTransfacClassManager.php
• ParseTransfacFactorManager.php
• ParseTransfacGeneManager.php
• ParseTransfacMatrixManager.php
• ParseTransfacSiteManager.php
• ParseUnigeneManager.php
• ParsedDataExtractor.php
• ParsedRecord.php
• PdbAtom.php
• PdbAtomInterface.php
• PdbHelix.php
• PdbHelixInterface.php
• PdbSheet.php
• PdbSheetInterface.php
• PhylogeneticNode.php
• Plasmid.php
• PlasmidFeature.php
• PlasmidFeatureRecord.php
• PlasmidRecord.php
• PlasmidRecordMapper.php
• PlasmidRecordMapperInterface.php
• PrositeDbRef.php
• PrositeDbRefInterface.php
• Protein.php
• ProteinInterface.php
• ProteinManager.php
• ProteinPropertiesCalculator.php
• ProteinPropertiesInterface.php
• ProteinReductionApi.php
• ProteinReductionApiAdapter.php
• ProteinReductionDTO.php

R

• RecordManager.php
• RecordStorageInterface.php
• Reference.php
• RestrictionCut.php
• RestrictionDigestInterface.php
• RestrictionDigestResult.php
• RestrictionEnd.php
• RestrictionEndCompatibilityInterface.php
• RestrictionEndCompatibilityManager.php
• RestrictionEnzymeCatalog.php
• RestrictionEnzymeCatalogInterface.php
• RestrictionEnzymeDefinition.php
• RestrictionEnzymeInterface.php
• RestrictionEnzymeManager.php
• RestrictionFragment.php
• RnaSequence.php

S

• SemiGlobalAligner.php
• SemiGlobalAlignerInterface.php
• Sequence.php
• SequenceAlignmentInterface.php
• SequenceAlignmentManager.php
• SequenceBuilder.php
• SequenceInterface.php
• SequenceManager.php
• SequenceMatchInterface.php
• SequenceMatchManager.php
• SequenceTrait.php
• SimpleMatchMismatchScoring.php
• SkewCalculator.php
• SkewCalculatorInterface.php
• SkewResult.php
• SmithWatermanAligner.php
• SmithWatermanAlignerInterface.php
• SpDatabank.php
• SrcForm.php
• Strand.php
• SubMatrix.php
• SubstitutionScoringInterface.php

T

• TmBaseStackingApi.php
• TmBaseStackingApiAdapter.php
• TmBaseStackingDTO.php
• TranslatesUnderGeneticCode.php
• TripletApi.php
• TripletApiAdapter.php
• TripletDTO.php
• TripletSpecieApi.php
• TripletSpecieApiAdapter.php
• TripletSpecieDTO.php
• TypeIIEndonucleaseApi.php
• TypeIIEndonucleaseApiAdapter.php
• TypeIIEndonucleaseDTO.php
• TypeIIbEndonucleaseApi.php
• TypeIIbEndonucleaseApiAdapter.php
• TypeIIbEndonucleaseDTO.php
• TypeIIsEndonucleaseApi.php
• TypeIIsEndonucleaseApiAdapter.php
• TypeIIsEndonucleaseDTO.php

U

• UnknownRestrictionEnzymeException.php
• UpgmaTreeBuilder.php
• UpgmaTreeBuilderInterface.php

V

• VcfImportResult.php
• VcfReader.php
• VcfReaderInterface.php
• VcfVariant.php
• VcfVariantRecord.php
• VcfVariantRecordMapper.php
• VcfVariantRecordMapperInterface.php
• VcfWriter.php
• VcfWriterInterface.php
• VendorApi.php
• VendorApiAdapter.php
• VendorDTO.php
• VendorLinkApi.php
• VendorLinkApiAdapter.php
• VendorLinkDTO.php