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