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python-biopython  1.60
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
Bio.PDB.HSExposure._AbstractHSExposure
Bio.Application._AbstractParameter
Bio.SeqIO.SffIO._AddTellHandle
Bio.Blast.NCBIStandalone._AlignmentConsumer
Bio.Application._Argument
Bio.GenBank._BaseGenBankConsumer
Bio.Blast.Applications._BlastAllOrPgpCommandLine
Bio.Blast.Applications._BlastCommandLine
Bio.Blast.NCBIStandalone._BlastConsumer
Bio.Blast.NCBIStandalone._BlastErrorConsumer
Bio.Graphics.BasicChromosome._ChromosomeComponent
Bio.Blast.NCBIStandalone._DatabaseReportConsumer
Bio.Blast.NCBIStandalone._DescriptionConsumer
Bio.Emboss.Applications._EmbossCommandLine
Bio.Emboss.Applications._EmbossMinimalCommandLine
Bio.GenBank._FeatureConsumer
Bio.PopGen.GenePop.Controller._FileIterator
Bio.PopGen.GenePop.Controller._GenePopCommandline
Bio.Blast.NCBIStandalone._HeaderConsumer
Bio.Blast.NCBIStandalone._HSPConsumer
Bio.GenBank.Scanner._ImgtScanner
Bio.SeqIO._index._IndexedSeqFileDict
Bio.Index._InMemoryIndex
Bio.SeqIO.InsdcIO._InsdcWriter
Bio.Blast.Applications._NcbibaseblastCommandline
Bio.Blast.Applications._Ncbiblast2SeqCommandline
Bio.Blast.Applications._NcbiblastCommandline
Bio.Blast.Applications._NcbiblastMain2SeqCommandline
Bio.Application._Option
Bio.Blast.NCBIStandalone._ParametersConsumer
BioSQL.DBUtils._PostgreSQL_dbutils
Bio.PDB.Polypeptide._PPBuilder
Bio.Blast.NCBIStandalone._PSIBlastConsumer
Bio.GenBank._RecordConsumer
Bio.SeqRecord._RestrictedDict
Bio.Blast.NCBIStandalone._Scanner
Bio.Search._SeqLength
Bio.Index._ShelveIndex
Bio.SeqIO._index._SQLiteManySeqFilesDict
Bio.Application._Switch
Bio.Blast.NCBIXML._XMLparser
test_PDB.A_ExceptionTest
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap
Bio.Application.AbstractCommandline
Bio.ParserSupport.AbstractConsumer
Bio.Restriction.Restriction.AbstractCut
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawerCLASSES
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer
Bio.ParserSupport.AbstractParser
Bio.SeqFeature.AbstractPosition
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap
Bio.GA.Selection.Abstract.AbstractSelection
Bio.HMM.Trainer.AbstractTrainer
test_HMMGeneral.AbstractTrainerTest
Bio.SubsMat.AcceptedReplacementsMatrix
Bio.Phylo.PhyloXML.Accession
Bio.Sequencing.Ace.ACEFileRecord
test_Ace.AceTestOne
test_Ace.AceTestThree
test_Ace.AceTestTwo
BioSQL.BioSeqDatabase.Adaptor
Bio.Sequencing.Ace.af
Bio.pairwise2.affine_penalty
Bio.SeqFeature.AfterPosition
Bio.Search.Algorithm
Bio.FSSP.fssp_rec.align
Bio.pairwise2.align
Bio.Motif.Applications._AlignAce.AlignAceCommandline
Bio.Align.Generic.Alignment
Bio.Wise.psw.Alignment
Bio.Blast.Record.Alignment
Bio.pairwise2.align.alignment_function
Bio.Wise.psw.AlignmentColumn
Bio.Wise.psw.AlignmentColumnFullException
Bio.CAPS.AlignmentHasDifferentLengthsError
Bio.AlignIO.Interfaces.AlignmentIterator
Bio.AlignIO.Interfaces.AlignmentWriter
Bio.Alphabet.Alphabet
Bio.Alphabet.AlphabetEncoder
Bio.Restriction.Restriction.Ambiguous
Bio.Data.CodonTable.AmbiguousCodonTable
Bio.Data.CodonTable.AmbiguousForwardTable
Bio.GA.Repair.Stabilizing.AmbiguousRepair
test_GARepair.AmbiguousRepairTest
Bio.Emboss.PrimerSearch.Amplifier
Bio.Restriction.Restriction.Analysis
Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment
Bio.Phylo.PhyloXML.Annotation
Bio.Application.ApplicationError
test_PopGen_DFDist.AppTest
test_PopGen_FDist.AppTest
test_PopGen_GenePop.AppTest
test_PopGen_GenePop_EasyController.AppTest
test_PopGen_SimCoal.AppTest
test_phyml_tool.AppTests
test_raxml_tool.AppTests
test_File.AsHandleTestCase
Bio.SCOP.Astral
test_SCOP_Astral.AstralTests
Bio.PopGen.Async.Async
Bio.PDB.Atom.Atom
Bio.PDB.NeighborSearch.Atom
test_PDB.Atom_Element
Bio.Graphics.Distribution.BarChartDistribution
test_GraphicsDistribution.BarChartTest
Bio.Phylo.PAML.baseml.Baseml
Bio.Phylo.PAML.baseml.BasemlError
test_PAML_tools.BasemlTest
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
Bio.HMM.Trainer.BaumWelchTrainer
Bio.SeqFeature.BeforePosition
Bio.SeqFeature.BetweenPosition
Bio.bgzf.BgzfReader
test_bgzf.BgzfTests
Bio.bgzf.BgzfWriter
Bio.Phylo.PhyloXML.BinaryCharacters
Bio.BiopythonDeprecationWarning
Bio.BiopythonParserWarning
Bio.BiopythonWarning
BioSQL.BioSeqDatabase.BioSeqDatabase
Bio.Blast.Record.Blast
Bio.Blast.Applications.BlastallCommandline
xbb_blastbg.BlastDisplayer
Bio.Blast.NCBIStandalone.BlastErrorParser
xbb_blast.BlastIt
Bio.Blast.NCBIStandalone.BlastParser
Bio.Blast.NCBIXML.BlastParser
Bio.Blast.Applications.BlastpgpCommandline
Bio.Blast.ParseBlastTable.BlastTableEntry
Bio.Blast.ParseBlastTable.BlastTableReader
Bio.Blast.ParseBlastTable.BlastTableRec
xbb_blastbg.BlastWorker
Bio.Nexus.Nexus.Block
Bio.Restriction.Restriction.Blunt
test_EmbossPhylipNew.BootstrapTests
Bio.Phylo.PhyloXML.BranchColor
Bio.Phylo.BaseTree.BranchColor
Bio.Sequencing.Ace.bs
setup.build_ext_biopython
setup.build_py_biopython
Bio.PDB.Polypeptide.CaPPBuilder
Bio.CAPS.CAPSMap
Bio.Nexus.Nodes.Chain
Bio.Crystal.Chain
Bio.PDB.Chain.Chain
Bio.Nexus.Nodes.ChainException
Bio.PDB.Dice.ChainSelector
test_Crystal.ChainTestCase
Bio.Nexus.Nexus.CharBuffer
test_NCBI_BLAST_tools.CheckCompleteArgList
Bio.Graphics.BasicChromosome.Chromosome
Bio.Graphics.DisplayRepresentation.ChromosomeCounts
test_GraphicsChromosome.ChromosomeCountTest
Bio.Graphics.BasicChromosome.ChromosomeSegment
Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer
Bio.Phylo.BaseTree.Clade
Bio.Phylo.Newick.Clade
Bio.Phylo.PhyloXML.Clade
Bio.Phylo.PhyloXML.CladeRelation
test_SCOP_Cla.ClaTests
test_BioSQL.ClosedLoopTest
Bio.AlignIO.ClustalIO.ClustalIterator
Bio.Align.Applications._ClustalOmega.ClustalOmegaCommandline
Bio.Align.Applications._Clustalw.ClustalwCommandline
Bio.AlignIO.ClustalIO.ClustalWriter
Bio.Phylo.PAML.codeml.Codeml
Bio.Phylo.PAML.codeml.CodemlError
test_PAML_tools.CodemlTest
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex
Bio.Data.CodonTable.CodonTable
test_GenomeDiagram.ColorsTest
Bio.Graphics.GenomeDiagram._Colors.ColorTranslator
Bio.Wise.psw.ColumnUnit
Bio.Nexus.Nexus.Commandline
Bio.Restriction.Restriction.Commercially_available
test_PAML_tools.Common
Bio.Graphics.Comparative.ComparativeScatterPlot
test_GraphicsBitmaps.ComparativeTest
test_GraphicsGeneral.ComparativeTest
Bio.Motif.Applications._AlignAce.CompareAceCommandline
run_tests.ComparisonTestCase
test_Compass.CompassTest
Bio.Phylo.PhyloXML.Confidence
Bio.Restriction._Update.Update.ConnectionError
Bio.ExPASy.ScanProsite.ContentHandler
Bio.Sequencing.Ace.Contig
Bio.GA.Mutation.Simple.ConversionMutation
test_GAMutation.ConversionTest
test_PopGen_FDist_nodepend.ConversionTest
test_AlignIO_convert.ConvertTests
test_SeqIO_convert.ConvertTests
test_PDB.CopyTests
Bio.Entrez.Parser.CorruptedXMLError
Bio.DocSQL.Create
test_GAOrganism.CreatePopulationTest
Bio.Graphics.GenomeDiagram._CrossLink.CrossLink
Bio.Crystal.Crystal
Bio.Crystal.CrystalError
test_Crystal.CrystalTestCase
Bio.Sequencing.Ace.ct
Bio.Search.Database
BioSQL.Loader.DatabaseLoader
BioSQL.Loader.DatabaseRemover
Bio.Blast.Record.DatabaseReport
Bio.Entrez.Parser.DataHandler
DataPoint
Bio.Phylo.PhyloXML.Date
getgene.DB_Index
BioSQL.BioSeq.DBSeq
BioSQL.BioSeq.DBSeqRecord
BioSQL.BioSeqDatabase.DBServer
debug_blast_parser.DebuggingConsumer
Bio.Restriction.Restriction.Defined
Bio.Blast.Record.Description
test_SCOP_Des.DesTests
Bio.Graphics.GenomeDiagram._Diagram.Diagram
test_GenomeDiagram.DiagramTest
test_Dialign_tool.DialignApplication
Bio.Align.Applications._Dialign.DialignCommandline
test_HMMCasino.DiceRollAlphabet
test_HMMCasino.DiceTypeAlphabet
Bio.pairwise2.dictionary_match
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder
Bio.Entrez.Parser.DictionaryElement
Bio.CAPS.DifferentialCutsite
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness
Bio.Emboss.Applications.DiffseqCommandline
Bio.PopGen.Async.DirectoryRetriever
Bio.PDB.Atom.DisorderedAtom
Bio.PDB.Entity.DisorderedEntityWrapper
Bio.PDB.Residue.DisorderedResidue
test_EmbossPhylipNew.DistanceTests
Bio.Phylo.PhyloXML.Distribution
Bio.Graphics.Distribution.DistributionPage
Bio.GA.Selection.Diversity.DiversitySelection
test_GASelection.DiversitySelectionTest
Bio.Alphabet.DNAAlphabet
xbb_search.DNAsearch
Bio.SCOP.Domain
Bio.Phylo.PhyloXML.DomainArchitecture
test_SCOP_Dom.DomTests
Bio.Sequencing.Ace.ds
Bio.PDB.DSSP.DSSP
test_BioSQL.DupLoadTest
Bio.PopGen.GenePop.EasyController.EasyController
test_Entrez.EFetchTest
test_Entrez.EGQueryTest
test_Entrez.EInfoTest
Bio.Emboss.Applications.EInvertedCommandline
test_Entrez.ELinkTest
Bio.SeqIO._index.EmblRandomAccess
Bio.GenBank.Scanner.EmblScanner
Bio.SeqIO.InsdcIO.EmblWriter
Bio.AlignIO.EmbossIO.EmbossIterator
Bio.AlignIO.EmbossIO.EmbossWriter
Bio.PDB.Entity.Entity
test_SeqIO_online.EntrezTests
test_Restriction.EnzymeComparison
test_Entrez.EPostTest
test_Entrez.ESearchTest
test_Entrez.ESpellTest
Bio.Emboss.Applications.Est2GenomeCommandline
test_Entrez.ESummaryTest
Bio.Emboss.Applications.ETandemCommandline
Bio.ParserSupport.EventGenerator
Bio.Phylo.PhyloXML.Events
Bio.SeqFeature.ExactPosition
Bio.NeuralNetwork.Training.ExampleManager
test_NNGeneral.ExampleManagerTest
test_SeqIO_online.ExPASyTests
Bio.SubsMat.ExpectedFrequencyMatrix
test_PDB.Exposure
Bio.PDB.HSExposure.ExposureCN
Bio.Alphabet.IUPAC.ExtendedIUPACDNA
Bio.Alphabet.IUPAC.ExtendedIUPACProteinProtein
Bio.Blast.Applications.FastacmdCommandline
Bio.SeqIO.FastaIO.FastaWriter
Bio.SeqIO.QualityIO.FastqIlluminaWriter
Bio.SeqIO.QualityIO.FastqPhredWriter
Bio.SeqIO._index.FastqRandomAccess
Bio.SeqIO.QualityIO.FastqSolexaWriter
Bio.Emboss.Applications.FConsenseCommandline
Bio.PopGen.FDist.Async.FDistAsync
Bio.PopGen.FDist.Controller.FDistController
Bio.Emboss.Applications.FDNADistCommandline
Bio.Emboss.Applications.FDNAParsCommandline
Bio.GenBank.Record.Feature
Bio.Graphics.GenomeDiagram._Feature.Feature
Bio.SeqFeature.FeatureLocation
Bio.GenBank.FeatureParser
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet
Bio.GenBank.utils.FeatureValueCleaner
test_SeqIO_features.FeatureWriting
Bio.FSSP.fssp_rec.fff_rec
test_PopGen_GenePop_nodepend.FileParserTest
Bio.PopGen.GenePop.FileParser.FileRecord
Bio.PopGen.Async.FileRetriever
Bio.Emboss.Applications.FNeighborCommandline
Bio.Restriction.Restriction.FormattedSeq
test_SeqIO.ForwardOnlyHandle
test_GACrossover.FourPointTest
Bio.Emboss.Applications.FProtDistCommandline
Bio.Emboss.Applications.FProtParsCommandline
Bio.PDB.FragmentMapper.Fragment
Bio.PDB.FragmentMapper.FragmentMapper
Bio.SubsMat.FreqTable.FreqTableA class to handle frequency tables Copyright Iddo Friedberg idoer.nosp@m.g@cc.nosp@m..huji.nosp@m..ac..nosp@m.il Biopython (http://biopython.org) license applies Methods to read a letter frequency or a letter count file: Example files for a DNA alphabet:
Bio.Emboss.Applications.FSeqBootCommandline
Bio.FSSP.FSSPTools.FSSPAlign
Bio.FSSP.FSSPAlignDict
Bio.FSSP.FSSPAlignRec
Bio.FSSP.FSSPHeader
Bio.FSSP.FSSPTools.FSSPMultAlign
Bio.FSSP.FSSPSumDict
Bio.FSSP.FSSPSumRec
Bio.Restriction._Update.Update.FtpNameError
Bio.Restriction._Update.Update.FtpPasswordError
Bio.Emboss.Applications.FTreeDistCommandline
Bio.Emboss.Applications.FuzznucCommandline
Bio.Alphabet.Gapped
Bio.SeqIO._index.GenBankRandomAccess
Bio.GenBank.Scanner.GenBankScanner
Bio.SeqIO.InsdcIO.GenBankWriter
Bio.PopGen.GenePop.Controller.GenePopController
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
test_Entrez.GeneralTests
Bio.GA.Evolver.GenerationEvolver
BioSQL.DBUtils.Generic_dbutils
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder
Bio.Pathway.Rep.Graph.Graph
Bio.Graphics.GenomeDiagram._Graph.GraphData
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet
test_GenomeDiagram.GraphTest
test_Pathway.GraphTestCase
Bio.Pathway.Rep.HashSet.HashSet
Bio.Alphabet.HasStopCodon
Bio.Blast.Record.Header
test_PDB.HeaderTests
Bio.Crystal.Hetero
test_Crystal.HeteroTestCase
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer
Bio.HMM.MarkovModel.HiddenMarkovModel
test_HMMGeneral.HiddenMarkovModelTest
test_SCOP_Hie.HieTests
Bio.Search.Hit
Bio.Search.HomologySeq
Bio.HotRand.HotCache
Bio.HotRand.HotRandom
Bio.Alphabet.Reduced.HPModel
Bio.PDB.HSExposure.HSExposureCA
Bio.PDB.HSExposure.HSExposureCB
Bio.Search.HSP
Bio.Blast.Record.HSP
Bio.Search.HSPSeq
Bio.Phylo.PhyloXML.Id
Bio.pairwise2.identity_match
Bio.Emboss.Applications.IepCommandline
Bio.SeqIO.InsdcIO.ImgtWriter
test_BioSQL.InDepthLoadTest
Bio.SCOP.Cla.Index
test_SeqIO_index.IndexDictTests
IndexList
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer
Bio.Emboss.PrimerSearch.InputRecord
Bio.GenBank.Scanner.InsdcScanner
Bio.DocSQL.Insert
setup.install_biopython
Bio.Entrez.Parser.IntegerElement
Bio.SeqIO._index.IntelliGeneticsRandomAccess
Bio.Pathway.Interaction
Bio.SeqIO.Interfaces.InterlacedSequenceIterator
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover
test_GACrossover.InterleaveTest
test_Phylo.IOTests
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint
Bio.DocSQL.IterationCursor
test_PDB.IterationTests
Bio.GenBank.Iterator
Bio.Blast.NCBIStandalone.Iterator
Bio.Alphabet.IUPAC.IUPACAmbiguousDNADNA
Bio.Alphabet.IUPAC.IUPACAmbiguousRNARNA
Bio.Alphabet.IUPAC.IUPACProtein
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA
KDTree
Bio.KDTree.KDTree.KDTree
test_KeyWList.KeyWListTest
Bio.kNN.kNN
Bio.HMM.Trainer.KnownStateTrainer
test_GenomeDiagram.LabelTest
test_HMMGeneral.LetterAlphabet
Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer
Bio.Graphics.Distribution.LineDistribution
Bio.Entrez.Parser.ListElement
test_BioSQL.LoaderTest
Bio.PopGen.Async.Local.Local
Bio.GenBank.LocationParserError
Bio.HMM.DynamicProgramming.LogDPAlgorithms
Bio.LogisticRegression.LogisticRegression
Bio.SubsMat.LogOddsMatrix
Bio.Blast.NCBIStandalone.LowQualityBlastError
test_Mafft_tool.MafftApplication
Bio.Align.Applications._Mafft.MafftCommandline
test_SeqIO_QualityIO.MappingTests
Bio.MarkovModel.MarkovModel
Bio.HMM.MarkovModel.MarkovModelBuilder
test_HMMGeneral.MarkovModelBuilderTest
Bio.MaxEntropy.MaxEntropy
Bio.Motif.Parsers.MEME.MEMEInstance
Bio.Motif.Parsers.MEME.MEMEMotif
Bio.Motif.Parsers.MEME.MEMERecord
Bio.Restriction.Restriction.Meth_Dep
Bio.Restriction.Restriction.Meth_Undep
test_PhyloXML.MethodTests
Bio.MissingExternalDependencyError
Bio.MissingPythonDependencyError
nextorf.MissingTable
test_Phylo.MixinTests
Bio.PDB.MMCIF2Dict.MMCIF2Dict
Bio.PDB.MMCIFParser.MMCIFParser
Bio.PDB.Model.Model
test_Chi2.ModTest
test_PAML_baseml.ModTest
test_PAML_codeml.ModTest
test_PAML_yn00.ModTest
Bio.Phylo.PhyloXML.MolSeq
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness
Bio.Motif._Motif.Motif
Bio.NeuralNetwork.Gene.Motif.MotifCoder
test_NNGene.MotifCoderTest
Bio.NeuralNetwork.Gene.Motif.MotifFinder
test_NNGene.MotifFinderTest
test_Motif.MotifTestPWM
test_Motif.MotifTestsBasic
Bio.Pathway.Rep.MultiGraph.MultiGraph
test_Pathway.MultiGraphTestCase
Bio.Blast.Record.MultipleAlignment
Bio.Align.MultipleSeqAlignment
Bio.Alphabet.Reduced.Murphy10
Bio.Alphabet.Reduced.Murphy15
Bio.Alphabet.Reduced.Murphy4
Bio.Alphabet.Reduced.Murphy8
test_Muscle_tool.MuscleApplication
Bio.Align.Applications._Muscle.MuscleCommandline
Bio.Seq.MutableSeq
test_GAMutation.MutationHelper
SeqGui.MyApp
Bio.File.SGMLStripper.MyParser
BioSQL.DBUtils.Mysql_dbutils
Bio.PDB.NACCESS.NACCESS
Bio.PDB.NACCESS.NACCESS_atomic
Bio.NaiveBayes.NaiveBayes
test_SeqIO_features.NC_000932
test_SeqIO_features.NC_005816
Bio.Blast.Applications.NcbiblastformatterCommandline
Bio.Blast.Applications.NcbiblastnCommandline
Bio.Blast.Applications.NcbiblastpCommandline
Bio.Blast.Applications.NcbiblastxCommandline
Bio.Data.CodonTable.NCBICodonTable
Bio.Data.CodonTable.NCBICodonTableDNA
Bio.Data.CodonTable.NCBICodonTableRNA
Bio.Blast.Applications.NcbipsiblastCommandline
Bio.Blast.Applications.NcbirpsblastCommandline
Bio.Blast.Applications.NcbirpstblastnCommandline
Bio.Blast.Applications.NcbitblastnCommandline
Bio.Blast.Applications.NcbitblastxCommandline
Bio.Emboss.Applications.NeedleallCommandline
Bio.Emboss.Applications.NeedleCommandline
Neighbor
Bio.PDB.NeighborSearch.NeighborSearch
test_PDB_KDTree.NeighborTest
Bio.Pathway.Network
Bio.Restriction._Update.RestrictionCompiler.newenzyme
Bio.Phylo.NewickIO.NewickError
nextorf.NextOrf
Bio.Nexus.Nexus.Nexus
Bio.Nexus.Nexus.NexusError
test_Nexus.NexusTest1
Bio.AlignIO.NexusIO.NexusWriter
test_GASelection.NoCrossover
Bio.Restriction.Restriction.NoCut
Bio.SCOP.Node
Bio.Nexus.Nodes.Node
Node
Bio.Nexus.Trees.NodeData
Bio.Nexus.Nodes.NodeException
Bio.DocSQL.NoInsertionError
test_GASelection.NoMutation
Bio.Restriction.Restriction.NonPalindromic
test_GASelection.NoRepair
test_GASelection.NoSelection
Bio.Restriction.Restriction.Not_available
Bio.Restriction.Restriction.NotDefined
xbb_utils.NotePad
Bio.Entrez.Parser.NotXMLError
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline
Bio.Alphabet.NucleotideAlphabetDNA
test_HMMGeneral.NumberAlphabet
Bio.SubsMat.ObservedFrequencyMatrix
test_SeqIO_index.OldIndexTest
Bio.Restriction.Restriction.OneCut
Bio.SeqFeature.OneOfPosition
Bio.GA.Organism.Organism
Bio.Graphics.BasicChromosome.Organism
test_GraphicsChromosome.OrganismGraphicTest
test_GraphicsChromosome.OrganismSubAnnotationsTest
test_GAOrganism.OrganismTest
Bio.Phylo.PhyloXML.Other
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
Bio.Emboss.PrimerSearch.OutputRecord
Bio.Restriction.Restriction.Ov3
Bio.Restriction.Restriction.Ov5
Bio.Restriction._Update.RestrictionCompiler.OverhangError
test_NCBI_BLAST_tools.Pairwise
test_Emboss.PairwiseAlignmentTests
Bio.Emboss.Applications.PalindromeCommandline
Bio.Restriction.Restriction.Palindromic
Bio.Phylo.PAML._paml.Paml
Bio.Phylo.PAML._paml.PamlError
Bio.Blast.Record.Parameters
SeqGui.ParamsPanel
Bio.Phylo.NewickIO.Parser
Bio.Phylo.PhyloXMLIO.Parser
Bio.ExPASy.ScanProsite.Parser
Bio.SeqIO.UniprotIO.Parser
test_MMCIF.ParseReal
test_PDB.ParseReal
Bio.GenBank.ParserFailureError
test_PopGen_FDist_nodepend.ParserTest
test_PopGen_GenePop_nodepend.ParserTest
test_PDB.ParseTest
test_PhyloXML.ParseTests
test_EmbossPhylipNew.ParsimonyTests
Bio.NeuralNetwork.Gene.Pattern.PatternIO
test_NNGene.PatternIOTest
Bio.NeuralNetwork.Gene.Pattern.PatternRepository
test_NNGene.PatternRepositoryTest
Bio.Alphabet.Reduced.PC5
Bio.PDB.PDBExceptions.PDBConstructionException
Bio.PDB.PDBExceptions.PDBConstructionWarning
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.PDBIO.PDBIO
Bio.PDB.PDBList.PDBList
Bio.PDB.PDBParser.PDBParser
Bio.NMR.xpktools.Peaklist
BioSQL.DBUtils.Pgdb_dbutils
test_Phd.PhdTest454
test_Phd.PhdTestOne
test_Phd.PhdTestSolexa
test_Phd.PhdTestTwo
Bio.SeqIO.PhdIO.PhdWriter
Bio.AlignIO.PhylipIO.PhylipIterator
Bio.AlignIO.PhylipIO.PhylipWriter
Bio.Phylo.PhyloXML.PhyloElement
Bio.Phylo.PhyloXML.Phylogeny
Bio.Phylo.PhyloXML.Phyloxml
Bio.Phylo.PhyloXMLIO.PhyloXMLError
Bio.Phylo.PhyloXML.PhyloXMLWarning
Bio.Phylo.Applications._Phyml.PhymlCommandline
Bio.Phylo.PhyloXML.Point
Bio.Phylo.PhyloXML.Polygon
Bio.PDB.Polypeptide.Polypeptide
Bio.FSSP.PosAlign
Bio.SeqFeature.PositionGap
Bio.PDB.Polypeptide.PPBuilder
test_Prank_tool.PrankApplication
Bio.Align.Applications._Prank.PrankCommandline
test_Prank_tool.PrankConversion
Bio.Emboss.Applications.Primer3Commandline
test_EmbossPrimer.Primer3ParseTest
Bio.Emboss.Primer3.Primers
Bio.Emboss.Applications.PrimerSearchCommandline
test_EmbossPrimer.PrimerSearchInputTest
test_EmbossPrimer.PrimersearchParseTest
Bio.Restriction.PrintFormat.PrintFormat
test_Probcons_tool.ProbconsApplication
Bio.Align.Applications._Probcons.ProbconsCommandline
Bio.Phylo.PhyloXML.Property
Bio.Alphabet.ProteinAlphabetProtein
Bio.SeqUtils.ProtParam.ProteinAnalysis
Bio.Phylo.PhyloXML.ProteinDomain
nextorf.ProteinX
Bio.UniGene.ProtsimLine
Bio.PDB.PSEA.PSEA
Bio.Blast.Record.PSIBlast
Bio.Blast.NCBIStandalone.PSIBlastParser
Bio.Align.AlignInfo.PSSM
BioSQL.DBUtils.Psycopg2_dbutils
PyNeighbor
PyNode
PyTree
Bio.Sequencing.Ace.qa
Bio.GenBank.Record.Qualifier
Bio.SeqIO.QualityIO.QualPhredWriter
test_GAQueens.QueensAlphabet
test_GAQueens.QueensCrossover
test_GAQueens.QueensMutation
test_GAQueens.QueensRepair
Bio.Search.Query
Bio.DocSQL.Query
Bio.DocSQL.QueryAll
Bio.DocSQL.QueryAllFirstItem
Bio.DocSQL.QueryGeneric
Bio.DocSQL.QueryRow
Bio.DocSQL.QuerySingle
Radius
test_SCOP_Raf.RafTests
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator
test_HotRand.RandomSequenceTest
Bio.Phylo.Applications._Raxml.RaxmlCommandline
Bio.Sequencing.Ace.rd
Bio.Pathway.Reaction
test_Pathway.ReactionTestCase
Bio.Sequencing.Ace.Reads
test_BioSQL.ReadTest
Bio.Restriction._Update.Update.RebaseUpdate
Bio.Cluster.Record
Bio.Compass.Record
Bio.Motif.Parsers.AlignAce.Record
Bio.Emboss.Primer3.Record
Bio.PopGen.GenePop.Record
Bio.SCOP.Hie.Record
Bio.PopGen.GenePop.LargeFileParser.Record
Bio.ExPASy.Enzyme.Record
Bio.ExPASy.Prodoc.Record
Bio.ExPASy.Prosite.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.Sequencing.Phd.Record
Bio.GenBank.Record.Record
Bio.KEGG.Compound.Record
Bio.SwissProt.Record
Bio.SwissProt.KeyWList.Record
Bio.UniGene.Record
Bio.Motif.Parsers.MAST.Record
Bio.PopGen.FDist.Record
Bio.Affy.CelFile.Record
Bio.KEGG.Enzyme.Record
Bio.ExPASy.ScanProsite.Record
Bio.Medline.Record
Bio.Geo.Record.Record
Bio.GenBank.RecordParser
test_PopGen_FDist_nodepend.RecordTest
test_PopGen_GenePop_nodepend.RecordTest
Bio.Phylo.PhyloXML.Reference
Bio.ExPASy.Prodoc.Reference
Bio.SeqFeature.Reference
Bio.GenBank.Record.Reference
Bio.SwissProt.Reference
Region
Bio.AlignIO.PhylipIO.RelaxedPhylipIterator
Bio.AlignIO.PhylipIO.RelaxedPhylipWriter
Bio.SCOP.Raf.Res
Bio.PDB.Residue.Residue
Bio.PDB.ResidueDepth.ResidueDepth
Bio.SCOP.Residues.Residues
test_SCOP_Residues.ResiduesTests
Bio.Restriction.Restriction.RestrictionBatch
test_Restriction.RestrictionBatches
Bio.Restriction.Restriction.RestrictionType
Bio.Alphabet.RNAAlphabetRNA
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection
test_GASelection.RouletteWheelSelectionTest
Bio.Blast.Record.Round
Bio.Blast.Applications.RpsBlastCommandline
Bio.Sequencing.Ace.rt
Bio.GA.Crossover.General.SafeFitnessCrossover
Bio.GA.Mutation.General.SafeFitnessMutation
test_GACrossover.SafeFitnessTest
test_GAMutation.SafeFitnessTest
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
test_HMMGeneral.ScaledDPAlgorithmsTest
Bio.NeuralNetwork.Gene.Schema.Schema
Bio.NeuralNetwork.Gene.Schema.SchemaCoder
test_NNGene.SchemaCoderTest
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet
Bio.NeuralNetwork.Gene.Schema.SchemaFactory
test_NNGene.SchemaFactoryTest
Bio.NeuralNetwork.Gene.Schema.SchemaFinder
test_NNGene.SchemaFinderTest
test_NNGene.SchemaMatchingTest
test_NNGene.SchemaTest
Bio.SCOP.Scop
test_SCOP_online.ScopSearch
test_SCOP_Scop.ScopTests
Bio.Motif.Thresholds.ScoreDistribution
Bio.Search.Search
Bio.Alphabet.SecondaryStructureOther per-sequence encodings
Bio.PDB.PDBIO.Select
Bio.Seq.Seq
Bio.SeqFeature.SeqFeature
test_SeqIO_features.SeqFeatureCreation
test_SeqIO_features.SeqFeatureExtractionWritingReading
Bio.SeqIO._index.SeqFileRandomAccess
SeqGui.SeqFrame
test_BioSQL.SeqInterfaceTest
Bio.SCOP.Raf.SeqMap
Bio.SCOP.Raf.SeqMapIndex
Bio.SubsMat.SeqMat
Bio.Emboss.Applications.SeqmatchallCommandline
SeqGui.SeqPanel
Bio.SeqRecord.SeqRecord
test_SeqRecord.SeqRecordCreation
test_SeqRecord.SeqRecordMethods
test_Emboss.SeqRetAlignIOTests
Bio.Emboss.Applications.SeqretCommandline
test_Emboss.SeqRetSeqIOTests
Bio.Phylo.PhyloXML.Sequence
Bio.SeqIO.Interfaces.SequenceIterator
Bio.UniGene.SequenceLine
Bio.Phylo.PhyloXML.SequenceRelation
Bio.SeqIO.Interfaces.SequenceWriter
Bio.AlignIO.Interfaces.SequentialAlignmentWriter
Bio.AlignIO.PhylipIO.SequentialPhylipIterator
Bio.AlignIO.PhylipIO.SequentialPhylipWriter
Bio.SeqIO._index.SequentialSeqFileRandomAccess
Bio.SeqIO.Interfaces.SequentialSequenceWriter
Bio.SeqIO.SeqXmlIO.SeqXmlIterator
Bio.SeqIO.SeqXmlIO.SeqXmlWriter
Bio.SeqIO._index.SffRandomAccess
Bio.SeqIO._index.SffTrimedRandomAccess
Bio.SeqIO.SffIO.SffWriter
Bio.File.SGMLStripper
Bio.ParserSupport.SGMLStrippingConsumer
Bio.Blast.NCBIStandalone.ShortQueryBlastError
test_GenomeDiagram.SigilsTest
Bio.NeuralNetwork.Gene.Signature.SignatureCoder
test_NNGene.SignatureCoderTest
Bio.NeuralNetwork.Gene.Signature.SignatureFinder
test_NNGene.SignatureFinderTest
Bio.PopGen.SimCoal.Async.SimCoalCache
Bio.PopGen.SimCoal.Cache.SimCoalCache
Bio.PopGen.SimCoal.Controller.SimCoalController
test_Muscle_tool.SimpleAlignTest
test_Restriction.SimpleEnzyme
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher
Bio.Alphabet.SingleLetterAlphabet
Bio.GA.Crossover.Point.SinglePointCrossover
test_GACrossover.SinglePointTest
Bio.GA.Mutation.Simple.SinglePositionMutation
test_GAMutation.SinglePositionTest
Bio.Graphics.BasicChromosome.SpacerSegment
Bio.PopGen.FDist.Async.SplitFDist
BioSQL.DBUtils.Sqlite_dbutils
Bio.Wise.dnal.Statistics
Bio.GA.Evolver.SteadyStateEvolver
Bio.Nexus.Nexus.StepMatrix
Bio.AlignIO.StockholmIO.StockholmIterator
Bio.AlignIO.StockholmIO.StockholmWriter
test_NNGeneral.StopTrainingTest
Bio.Emboss.Applications.StretcherCommandline
Bio.Entrez.Parser.StringElement
Bio.File.StringHandle
test_Seq_objs.StringMethodTests
Bio.PDB.Structure.Structure
Bio.PDB.StructureAlignment.StructureAlignment
Bio.PDB.StructureBuilder.StructureBuilder
Bio.Entrez.Parser.StructureElement
Bio.UniGene.STSLine
Bio.SubsMat.SubstitutionMatrix
Bio.Align.AlignInfo.SummaryInfo
Bio.PDB.Superimposer.Superimposer
Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
Bio.SeqIO._index.SwissRandomAccess
Bio.Pathway.System
Bio.Search.TableInfo
Bio.SeqIO._index.TabRandomAccess
Bio.SeqIO.TabIO.TabWriter
Bio.ParserSupport.TaggingConsumer
Bio.Phylo.PhyloXML.Taxonomy
test_TCoffee_tool.TCoffeeApplication
Bio.Align.Applications._TCoffee.TCoffeeCommandline
Bio.Graphics.BasicChromosome.TelomereSegment
test_PopGen_SimCoal_nodepend.TemplateTest
setup.test_biopython
test_lowess.test_lowess
test_SeqIO_AbiIO.TestAbi
test_SeqIO_AbiIO.TestAbiFake
test_SeqIO_AbiIO.TestAbiWrongMode
test_GARepair.TestAlphabet
test_GACrossover.TestAlphabet
test_GAOrganism.TestAlphabet
test_GAMutation.TestAlphabet
test_GASelection.TestAlphabet
test_NCBITextParser.TestBlastRecord
test_CAPS.TestCAPS
test_Cluster.TestCluster
test_GACrossover.TestCrossover
test_SeqIO_SeqXML.TestDetailedRead
test_Enzyme.TestEnzyme
test_SeqIO_QualityIO.TestFastqErrors
test_ParserSupport.TestHandleTaggingConsumer
test_kNN.TestKNN
test_LogisticRegression.TestLogisticRegression
test_MarkovModel.TestMarkovModel
test_Motif.TestMAST
test_Medline.TestMedline
test_Motif.TestMEME
test_GAMutation.TestMutator
test_NCBIStandalone.TestNCBIStandalone
test_NCBITextParser.TestNCBITextParser
test_NCBIXML.TestNCBIXML
test_pairwise2.TestPairwiseExtendPenalty
test_pairwise2.TestPairwiseGlobal
test_pairwise2.TestPairwiseLocal
test_pairwise2.TestPairwiseMatchDictionary
test_pairwise2.TestPairwiseOneCharacter
test_pairwise2.TestPairwiseOpenPenalty
test_pairwise2.TestPairwisePenalizeEndgaps
test_pairwise2.TestPairwisePenalizeExtendWhenOpening
test_pairwise2.TestPairwiseSeparateGapPenalties
test_pairwise2.TestPairwiseSeparateGapPenaltiesWithExtension
test_prodoc.TestProdocParse
test_prodoc.TestProdocRead
test_prosite2.TestPrositeRead
test_prosite1.TestPrositeRead
test_psw.TestPSW
test_SeqIO_QualityIO.TestQual
test_SeqIO_SeqXML.TestReadAndWrite
test_SeqIO_SeqXML.TestReadCorruptFiles
test_SeqIO_QualityIO.TestReadWrite
test_SeqIO_QualityIO.TestReferenceFastqConversions
test_SeqIO_QualityIO.TestReferenceSffConversions
run_tests.TestRunner
test_SeqIO_SeqXML.TestSimpleRead
test_SwissProt.TestSwissProt
test_trie.TestTrie
test_trie.TestTrieFind
test_SffIO.TestUAN
test_UniGene.TestUniGene
test_Uniprot.TestUniprot
test_Wise.TestWise
test_Wise.TestWiseDryRun
test_SeqIO_QualityIO.TestWriteRead
test_SeqIO_features.TestWriteRead
Bio.Alphabet.ThreeLetterProtein
test_SeqIO_FastaIO.TitleFunctions
test_TogoWS.TogoConvert
test_TogoWS.TogoEntry
test_TogoWS.TogoFields
test_TogoWS.TogoSearch
Bio.GA.Selection.Tournament.TournamentSelection
test_GASelection.TournamentSelectionTest
Bio.Graphics.GenomeDiagram._Track.Track
test_GenomeDiagram.TrackTestEnd of utility functions for graph plotting #
Bio.NeuralNetwork.Training.TrainingExample
Bio.HMM.Trainer.TrainingSequence
Bio.Emboss.Applications.TranalignCommandline
test_BioSQL.TransferTest
test_PDB.TransformTests
Transition
Bio.Data.CodonTable.TranslationError
test_Emboss.TranslationTests
Bio.Nexus.Trees.Tree
Bio.Phylo.Newick.Tree
Bio.Phylo.BaseTree.Tree
test_EmbossPhylipNew.TreeComparisonTests
Bio.Phylo.BaseTree.TreeElement
Bio.Nexus.Trees.TreeError
Bio.Phylo.BaseTree.TreeMixin
test_Phylo.TreeTests
test_PhyloXML.TreeTests
Trie
trieobject
test_Tutorial.TutorialDocTestHolder
test_Tutorial.TutorialTestCase
Bio.GA.Crossover.GeneralPoint.TwoCrossover
Bio.Restriction.Restriction.TwoCuts
Bio.GA.Crossover.TwoPoint.TwoPointCrossover
test_GACrossover.TwoPointTest
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler
Bio.SeqFeature.UncertainPosition
Bio.File.UndoHandle
Bio.Entrez.Parser.UnicodeElement
Bio.GA.Crossover.Uniform.UniformCrossover
test_GACrossover.UniformTest
Bio.UniGene.UniGene.UniGeneParser
Bio.SeqIO._index.UniprotRandomAccess
Bio.Restriction.Restriction.Unknown
Bio.SeqFeature.UnknownPosition
Bio.Seq.UnknownSeq
Bio.DocSQL.Update
Bio.Phylo.PhyloXML.Uri
test_PopGen_GenePop_nodepend.UtilsTest
test_Phylo_depend.UtilTests
Bio.Entrez.Parser.ValidationError
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop
Bio.PDB.Vector.Vector
Bio.Sequencing.Ace.wa
Bio.Emboss.Applications.WaterCommandline
Bio.SeqFeature.WithinPosition
Bio.Sequencing.Ace.wr
Bio.Phylo.NewickIO.Writer
Bio.Phylo.PhyloXMLIO.Writer
test_SeqIO_write.WriterTests
test_PhyloXML.WriterTests
xbb_sequence.xbb_sequence
xbb_translations.xbb_translations
xbb_widget.xbb_widget
xbb_help.xbbtools_help
xbb_search.XDNAsearch
Bio.SeqIO.SeqXmlIO.XMLRecordIterator
Bio.NMR.xpktools.XpkEntry
Bio.Phylo.PAML.yn00.Yn00
Bio.Phylo.PAML.yn00.Yn00Error
test_PAML_tools.Yn00Test
yy_buffer_state