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  A  
DisorderedResidue (Bio::PDB::Residue)   
  L  
PSSM (Bio::Align::AlignInfo)   SinglePointTest (test_GACrossover)   
AbstractCommandline (Bio::Application)   DistanceTests (test_EmbossPhylipNew)   LabelTest (test_GenomeDiagram)   
  Q  
SinglePositionMutation (Bio::GA::Mutation::Simple)   
AbstractConsumer (Bio::ParserSupport)   DistributionPage (Bio::Graphics::Distribution)   LetterAlphabet (test_HMMGeneral)   qa (Bio::Sequencing::Ace)   SinglePositionTest (test_GAMutation)   
AbstractCut (Bio::Restriction::Restriction)   DiversitySelection (Bio::GA::Selection::Diversity)   LinearDrawer (Bio::Graphics::GenomeDiagram::_LinearDrawer)   QualDict (Bio::SeqIO::_index)   SplitFDist (Bio::PopGen::FDist::Async)   
AbstractDPAlgorithms (Bio::HMM::DynamicProgramming)   DiversitySelectionTest (test_GASelection)   LineDistribution (Bio::Graphics::Distribution)   Qualifier (Bio::GenBank::Record)   Sqlite_dbutils (BioSQL::DBUtils)   
AbstractDrawer (Bio::Graphics::GenomeDiagram::_AbstractDrawer)   DNAStrand (test_MarkovModel)   LoaderTest (test_BioSQL)   QualPhredWriter (Bio::SeqIO::QualityIO)   Statistics (Bio::Wise::dnal)   
AbstractLayer (Bio::NeuralNetwork::BackPropagation::Layer)   Domain (Bio::SCOP)   Local (Bio::PopGen::Async::Local)   QueensCrossover (test_GAQueens)   SteadyStateEvolver (Bio::GA::Evolver)   
AbstractParser (Bio::ParserSupport)   ds (Bio::Sequencing::Ace)   Location (Bio::GFF::easy)   QueensMutation (test_GAQueens)   StepMatrix (Bio::Nexus::Nexus)   
AbstractPosition (Bio::SeqFeature)   DSSP (Bio::PDB::DSSP)   LocationFromCoords (Bio::GFF::easy)   QueensRepair (test_GAQueens)   StockholmIterator (Bio::AlignIO::StockholmIO)   
AbstractSelection (Bio::GA::Selection::Abstract)   DupLoadTest (test_BioSQL)   LocationFromString (Bio::GFF::easy)   Query (Bio::DocSQL)   StockholmWriter (Bio::AlignIO::StockholmIO)   
AbstractTrainer (Bio::HMM::Trainer)   
  E  
LocationJoin (Bio::GFF::easy)   
  R  
StopTrainingTest (test_NNGeneral)   
AcceptedReplacementsMatrix (Bio::SubsMat)   EConsenseCommandline (Bio::Emboss::Applications)   LocationParserError (Bio::GenBank)   RandomMotifGenerator (Bio::NeuralNetwork::Gene::Schema)   Structure (Bio::PDB::Structure)   
AceDict (Bio::SeqIO::_index)   EFetchTest (test_Entrez)   LogDPAlgorithms (Bio::HMM::DynamicProgramming)   RandomSequenceTest (test_HotRand)   StructureAlignment (Bio::PDB::StructureAlignment)   
ACEFileRecord (Bio::Sequencing::Ace)   EGQueryTest (test_Entrez)   LogisticRegression (Bio::LogisticRegression)   rd (Bio::Sequencing::Ace)   StructureBuilder (Bio::PDB::StructureBuilder)   
AceTestThree (test_Ace)   EInfoTest (test_Entrez)   LogOddsMatrix (Bio::SubsMat)   Reaction (Bio::Pathway)   STSLine (Bio::UniGene)   
AceTestTwo (test_Ace)   EInvertedCommandline (Bio::Emboss::Applications)   LowQualityBlastError (Bio::Blast::NCBIStandalone)   Reads (Bio::Sequencing::Ace)   SubstitutionMatrix (Bio::SubsMat)   
af (Bio::Sequencing::Ace)   ELinkTest (test_Entrez)   
  M  
ReadTest (test_BioSQL)   SummaryInfo (Bio::Align::AlignInfo)   
affine_penalty (Bio::pairwise2)   EmblDict (Bio::SeqIO::_index)   MafftCommandline (Bio::Align::Applications::_Mafft)   Record (Bio::Compass)   Superimposer (Bio::PDB::Superimposer)   
AfterPosition (Bio::SeqFeature)   EmblScanner (Bio::GenBank::Scanner)   MarkovModelBuilder (Bio::HMM::MarkovModel)   Record (Bio::PopGen::GenePop)   Surrogate (Bio::GFF::GenericTools)   
align (Bio::pairwise2)   EmbossIterator (Bio::AlignIO::EmbossIO)   MASTParser (Bio::Motif::Parsers::MEME)   Record (Bio::PopGen::FDist)   SVDSuperimposer (Bio::SVDSuperimposer::SVDSuperimposer)   
align::alignment_function (Bio::pairwise2)   EmbossWriter (Bio::AlignIO::EmbossIO)   MASTParser (Bio::MEME::Parser)   Record (Bio::Cluster)   SwissDict (Bio::SeqIO::_index)   
AlignAceCommandline (Bio::Motif::Applications::_AlignAce)   ENeighborCommandline (Bio::Emboss::Applications)   MASTRecord (Bio::Motif::Parsers::MEME)   Record (Bio::SCOP::Dom)   System (Bio::Pathway)   
AlignAceCommandline (Bio::AlignAce::Applications)   Entity (Bio::PDB::Entity)   MASTRecord (Bio::MEME::Parser)   Record (Bio::ExPASy::Prodoc)   
  T  
AlignAceConsumer (Bio::Motif::Parsers::AlignAce)   EnzymeComparison (test_Restriction)   MaxEntropy (Bio::MaxEntropy)   Record (Bio::SwissProt::KeyWList)   TabDict (Bio::SeqIO::_index)   
AlignAceConsumer (Bio::AlignAce::Parser)   EPostTest (test_Entrez)   MEMEInstance (Bio::Motif::Parsers::MEME)   Record (Bio::ExPASy::Prosite)   TabWriter (Bio::SeqIO::TabIO)   
AlignAceParser (Bio::Motif::Parsers::AlignAce)   EProtDistCommandline (Bio::Emboss::Applications)   MEMEMotif (Bio::Motif::Parsers::MEME)   Record (Bio::Sequencing::Phd)   TaggingConsumer (Bio::ParserSupport)   
AlignAceParser (Bio::AlignAce::Parser)   EProtParsCommandline (Bio::Emboss::Applications)   MEMEMotif (Bio::MEME::Motif)   Record (Bio::Geo::Record)   TCoffeeCommandline (Bio::Align::Applications::_TCoffee)   
AlignAceScanner (Bio::AlignAce::Scanner)   ESearchTest (test_Entrez)   MEMEParser (Bio::Motif::Parsers::MEME)   Record (Bio::ExPASy::Enzyme)   TelomereSegment (Bio::Graphics::BasicChromosome)   
AlignAceScanner (Bio::Motif::Parsers::AlignAce)   ESeqBootCommandline (Bio::Emboss::Applications)   MEMEParser (Bio::MEME::Parser)   Record (Bio::Emboss::Primer3)   test_biopython (setup)   
Alignment (Bio::Blast::Record)   ESpellTest (test_Entrez)   MEMERecord (Bio::Motif::Parsers::MEME)   Record (Bio::KEGG::Enzyme)   TestAlphabet (test_GAOrganism)   
Alignment (Bio::Align::Generic)   Est2GenomeCommandline (Bio::Emboss::Applications)   MEMERecord (Bio::MEME::Parser)   Record (Bio::SwissProt)   TestAlphabet (test_GARepair)   
AlignmentIterator (Bio::AlignIO::Interfaces)   ESummaryTest (test_Entrez)   Meth_Dep (Bio::Restriction::Restriction)   Record (Bio::Medline)   TestAlphabet (test_GAMutation)   
AlignmentWriter (Bio::AlignIO::Interfaces)   ETandemCommandline (Bio::Emboss::Applications)   Meth_Undep (Bio::Restriction::Restriction)   Record (Bio::KEGG::Compound)   TestAlphabet (test_GASelection)   
Ambiguous (Bio::Restriction::Restriction)   EventGenerator (Bio::ParserSupport)   Model (Bio::PDB::Model)   Record (Bio::UniGene)   TestAlphabet (test_GACrossover)   
AmbiguousRepair (Bio::GA::Repair::Stabilizing)   ExactPosition (Bio::SeqFeature)   MostCountSchemaFitness (Bio::NeuralNetwork::Gene::Schema)   Record (Bio::Motif::Parsers::MAST)   TestCrossover (test_GACrossover)   
AmbiguousRepairTest (test_GARepair)   ExampleManager (Bio::NeuralNetwork::Training)   Motif (Bio::Motif::_Motif)   Record (Bio::SwissProt::SProt)   TestFastqErrors (test_SeqIO_QualityIO)   
Amplifier (Bio::Emboss::PrimerSearch)   ExampleManagerTest (test_NNGeneral)   Motif (Bio::MEME::Motif)   Record (Bio::Prosite)   TestMutator (test_GAMutation)   
AppendableListDictionary (Bio::GFF::GenericTools)   ExpectedFrequencyMatrix (Bio::SubsMat)   Motif (Bio::AlignAce::Motif)   Record (Bio::Fasta)   TestQual (test_SeqIO_QualityIO)   
ApplicationResult (Bio::Application)   ExtendedIUPACDNA (Bio::Alphabet::IUPAC)   MotifCoder (Bio::NeuralNetwork::Gene::Motif)   Record (Bio::SCOP::Hie)   TestReadWrite (test_SeqIO_QualityIO)   
AppTest (test_PopGen_SimCoal)   ExtendedIUPACProtein (Bio::Alphabet::IUPAC)   MotifCoderTest (test_NNGene)   Record (Bio::SCOP::Des)   TestReferenceConversions (test_SeqIO_QualityIO)   
AppTest (test_PopGen_GenePop_EasyController)   
  F  
MotifFinder (Bio::NeuralNetwork::Gene::Motif)   Record (Bio::SCOP::Cla)   TestWriteRead (test_SeqIO_QualityIO)   
AppTest (test_PopGen_GenePop)   FastaAlignment (Bio::Fasta::FastaAlign)   MotifFinderTest (test_NNGene)   Record (Bio::GenBank::Record)   TestWriteRead (test_SeqIO_features)   
AppTest (test_PopGen_FDist)   FastacmdCommandline (Bio::Blast::Applications)   MultiGraph (Bio::Pathway::Rep::MultiGraph)   Record (Bio::Prosite::Prodoc)   TitleFunctions (test_SeqIO_FastaIO)   
ArgsParser (Bio::GFF::GenericTools)   FastaDict (Bio::SeqIO::_index)   MultipleAlignCL (Bio::Clustalw)   Record (Bio::ExPASy::ScanProsite)   TournamentSelection (Bio::GA::Selection::Tournament)   
Astral (Bio::SCOP)   FastaM10Iterator (Bio::AlignIO::FastaIO)   MultipleAlignment (Bio::Blast::Record)   Record (Bio::Affy::CelFile)   TournamentSelectionTest (test_GASelection)   
Async (Bio::PopGen::Async)   FastaWriter (Bio::SeqIO::FastaIO)   MuscleCommandline (Bio::Align::Applications::_Muscle)   RecordParser (Bio::SwissProt::SProt)   Track (Bio::Graphics::GenomeDiagram::_Track)   
  B  
FastqIlluminaDict (Bio::SeqIO::_index)   MutableSeq (Bio::Seq)   RecordParser (Bio::Fasta)   TrainingExample (Bio::NeuralNetwork::Training)   
BarChartDistribution (Bio::Graphics::Distribution)   FastqPhredWriter (Bio::SeqIO::QualityIO)   MutationHelper (test_GAMutation)   RecordParser (Bio::PopGen::FDist)   TrainingSequence (Bio::HMM::Trainer)   
BarChartTest (test_GraphicsDistribution)   FastqSangerDict (Bio::SeqIO::_index)   
  N  
RecordParser (Bio::Prosite::Prodoc)   TranalignCommandline (Bio::Emboss::Applications)   
BasicNetwork (Bio::NeuralNetwork::BackPropagation::Network)   FastqSolexaDict (Bio::SeqIO::_index)   NaiveBayes (Bio::NaiveBayes)   RecordParser (Bio::Prosite)   TransferTest (test_BioSQL)   
BaumWelchTrainer (Bio::HMM::Trainer)   FConsenseCommandline (Bio::Emboss::Applications)   NcbiblastnCommandline (Bio::Blast::Applications)   RecordParser (Bio::PopGen::GenePop)   TranslationTests (test_Emboss)   
BeforePosition (Bio::SeqFeature)   FDistAsync (Bio::PopGen::FDist::Async)   NcbiblastpCommandline (Bio::Blast::Applications)   RecordParser (Bio::GenBank)   Tree (Bio::Nexus::Trees)   
BetweenPosition (Bio::SeqFeature)   FDNADistCommandline (Bio::Emboss::Applications)   NcbiblastxCommandline (Bio::Blast::Applications)   RecordParser (Bio::Compass)   TreeComparisonTests (test_EmbossPhylipNew)   
Blast (Bio::Blast::Record)   FDNAParsCommandline (Bio::Emboss::Applications)   NCBIDictionary (Bio::GenBank)   Reference (Bio::SwissProt::SProt)   TwoCrossover (Bio::GA::Crossover::GeneralPoint)   
BlastallCommandline (Bio::Blast::Applications)   Feature (Bio::Graphics::GenomeDiagram::_Feature)   NcbipsiblastCommandline (Bio::Blast::Applications)   Reference (Bio::ExPASy::Prodoc)   TwoCuts (Bio::Restriction::Restriction)   
BlastErrorParser (Bio::Blast::NCBIStandalone)   Feature (Bio::GFF)   NcbirpsblastCommandline (Bio::Blast::Applications)   Reference (Bio::GenBank::Record)   TwoPointCrossover (Bio::GA::Crossover::TwoPoint)   
BlastParser (Bio::Blast::NCBIXML)   Feature (Bio::GenBank::Record)   NcbirpstblastnCommandline (Bio::Blast::Applications)   Reference (Bio::Prosite::Prodoc)   TwoPointTest (test_GACrossover)   
BlastParser (Bio::Blast::NCBIStandalone)   FeatureAggregate (Bio::GFF)   NcbitblastnCommandline (Bio::Blast::Applications)   Reference (Bio::SwissProt)   TypeCompiler (Bio::Restriction::_Update::RestrictionCompiler)   
BlastpgpCommandline (Bio::Blast::Applications)   FeatureDict (Bio::GFF::easy)   NcbitblastxCommandline (Bio::Blast::Applications)   Reference (Bio::SeqFeature)   
  U  
Block (Bio::Nexus::Nexus)   FeatureLocation (Bio::SeqFeature)   NeedleCommandline (Bio::Emboss::Applications)   Res (Bio::SCOP::Raf)   UndoHandle (Bio::File)   
Blunt (Bio::Restriction::Restriction)   FeatureParser (Bio::GenBank)   NeighborSearch (Bio::PDB::NeighborSearch)   Residue (Bio::PDB::Residue)   UniformCrossover (Bio::GA::Crossover::Uniform)   
BootstrapTests (test_EmbossPhylipNew)   FeatureQuery (Bio::GFF)   NetCatch (Bio::NetCatch)   ResidueDepth (Bio::PDB::ResidueDepth)   UniformTest (test_GACrossover)   
bs (Bio::Sequencing::Ace)   FeatureQueryRow (Bio::GFF)   Network (Bio::Pathway)   Residues (Bio::SCOP::Residues)   UnigeneProtsimRecord (Bio::UniGene)   
  C  
FeatureSet (Bio::Graphics::GenomeDiagram::_FeatureSet)   newenzyme (Bio::Restriction::_Update::RestrictionCompiler)   RestrictionBatches (test_Restriction)   UnigeneRecord (Bio::UniGene)   
CaPPBuilder (Bio::PDB::Polypeptide)   FeatureValueCleaner (Bio::GenBank::utils)   NexusWriter (Bio::AlignIO::NexusIO)   RestrictionType (Bio::Restriction::Restriction)   UnigeneSequenceRecord (Bio::UniGene)   
CAPSMap (Bio::CAPS)   FileRetriever (Bio::PopGen::Async)   NoCrossover (test_GASelection)   RetrieveSeqname (Bio::GFF)   UnigeneSTSRecord (Bio::UniGene)   
CelParser (Bio::Affy::CelFile)   FNeighborCommandline (Bio::Emboss::Applications)   NoCut (Bio::Restriction::Restriction)   RouletteWheelSelection (Bio::GA::Selection::RouletteWheel)   Unknown (Bio::Restriction::Restriction)   
CelRecord (Bio::Affy::CelFile)   FormatConverter (Bio::Align::FormatConvert)   Node (Bio::Nexus::Nodes)   RouletteWheelSelectionTest (test_GASelection)   UnknownSeq (Bio::Seq)   
CelScanner (Bio::Affy::CelFile)   FormattedSeq (Bio::Restriction::Restriction)   Node (Bio::SCOP)   Round (Bio::Blast::Record)   
  V  
Chain (Bio::Nexus::Nodes)   FourPointTest (test_GACrossover)   NodeData (Bio::Nexus::Trees)   RpsBlastCommandline (Bio::Blast::Applications)   ValidationIncreaseStop (Bio::NeuralNetwork::StopTraining)   
ChainSelector (Bio::PDB::Dice)   FProtDistCommandline (Bio::Emboss::Applications)   NoMutation (test_GASelection)   rt (Bio::Sequencing::Ace)   
  W  
CharBuffer (Bio::Nexus::Nexus)   FProtParsCommandline (Bio::Emboss::Applications)   NonPalindromic (Bio::Restriction::Restriction)   
  S  
wa (Bio::Sequencing::Ace)   
Chromosome (Bio::Graphics::BasicChromosome)   Fragment (Bio::PDB::FragmentMapper)   NoRepair (test_GASelection)   SafeFitnessCrossover (Bio::GA::Crossover::General)   WaterCommandline (Bio::Emboss::Applications)   
ChromosomeCounts (Bio::Graphics::DisplayRepresentation)   FragmentMapper (Bio::PDB::FragmentMapper)   NoSelection (test_GASelection)   SafeFitnessMutation (Bio::GA::Mutation::General)   WithinPosition (Bio::SeqFeature)   
ChromosomeCountTest (test_GraphicsChromosome)   FSeqBootCommandline (Bio::Emboss::Applications)   Not_available (Bio::Restriction::Restriction)   SafeFitnessTest (test_GACrossover)   wr (Bio::Sequencing::Ace)   
ChromosomeSegment (Bio::Graphics::BasicChromosome)   FSSPSumRec (Bio::FSSP)   NotDefined (Bio::Restriction::Restriction)   SafeFitnessTest (test_GAMutation)   
  _  
CircularDrawer (Bio::Graphics::GenomeDiagram::_CircularDrawer)   FTreeDistCommandline (Bio::Emboss::Applications)   NovoalignCommandline (Bio::Sequencing::Applications::_Novoalign)   ScaledDPAlgorithms (Bio::HMM::DynamicProgramming)   _AbstractHSExposure (Bio::PDB::HSExposure)   
ClosedLoopTest (test_BioSQL)   FuzznucCommandline (Bio::Emboss::Applications)   NumberAlphabet (test_HMMGeneral)   Schema (Bio::NeuralNetwork::Gene::Schema)   _AbstractParameter (Bio::Application)   
ClustalAlignment (Bio::Clustalw)   
  G  
  O  
SchemaCoder (Bio::NeuralNetwork::Gene::Schema)   _Argument (Bio::Application)   
ClustalIterator (Bio::AlignIO::ClustalIO)   GenBankDict (Bio::SeqIO::_index)   ObservedFrequencyMatrix (Bio::SubsMat)   SchemaCoderTest (test_NNGene)   _BaseGenBankConsumer (Bio::GenBank)   
ClustalwCommandline (Bio::Align::Applications::_Clustalw)   GenBankScanner (Bio::GenBank::Scanner)   OneCut (Bio::Restriction::Restriction)   SchemaDNAAlphabet (Bio::NeuralNetwork::Gene::Schema)   _BlastAllOrPgpCommandLine (Bio::Blast::Applications)   
ClustalWriter (Bio::AlignIO::ClustalIO)   GeneralPointCrossover (Bio::GA::Crossover::GeneralPoint)   OneOfPosition (Bio::SeqFeature)   SchemaFactory (Bio::NeuralNetwork::Gene::Schema)   _BlastCommandLine (Bio::Blast::Applications)   
CodonAdaptationIndex (Bio::SeqUtils::CodonUsage)   GenerationEvolver (Bio::GA::Evolver)   Organism (Bio::GA::Organism)   SchemaFactoryTest (test_NNGene)   _ChromosomeComponent (Bio::Graphics::BasicChromosome)   
ColorTranslator (Bio::Graphics::GenomeDiagram::_Colors)   GeneticAlgorithmFinder (Bio::NeuralNetwork::Gene::Schema)   Organism (Bio::Graphics::BasicChromosome)   SchemaFinder (Bio::NeuralNetwork::Gene::Schema)   _EmbossCommandLine (Bio::Emboss::Applications)   
Commandline (Bio::Nexus::Nexus)   Graph (Bio::Pathway::Rep::Graph)   OrganismGraphicTest (test_GraphicsChromosome)   SchemaFinderTest (test_NNGene)   _EmbossMinimalCommandLine (Bio::Emboss::Applications)   
ComparativeScatterPlot (Bio::Graphics::Comparative)   GraphData (Bio::Graphics::GenomeDiagram::_Graph)   OrganismTest (test_GAOrganism)   SchemaMatchingTest (test_NNGene)   _FastqSeqFileDict (Bio::SeqIO::_index)   
ComparativeTest (test_GraphicsGeneral)   GraphSet (Bio::Graphics::GenomeDiagram::_GraphSet)   OutputRecord (Bio::Emboss::PrimerSearch)   SchemaTest (test_NNGene)   _FeatureConsumer (Bio::GenBank)   
ComparativeTest (test_GraphicsBitmaps)   
  H  
Ov3 (Bio::Restriction::Restriction)   Scop (Bio::SCOP)   _FileIterator (Bio::PopGen::GenePop::Controller)   
CompareAceCommandline (Bio::Motif::Applications::_AlignAce)   HashSet (Bio::Pathway::Rep::HashSet)   Ov5 (Bio::Restriction::Restriction)   ScoreDistribution (Bio::Motif::Thresholds)   _GenePopCommandline (Bio::PopGen::GenePop::Controller)   
CompareAceCommandline (Bio::AlignAce::Applications)   Header (Bio::Blast::Record)   OverhangError (Bio::Restriction::_Update::RestrictionCompiler)   Segment (Bio::GFF)   _IndexedSeqFileDict (Bio::SeqIO::_index)   
CompareAceConsumer (Bio::AlignAce::Parser)   Hetero (Bio::Crystal)   
  P  
Select (Bio::PDB::PDBIO)   _InMemoryIndex (Bio::Index)   
CompareAceConsumer (Bio::Motif::Parsers::AlignAce)   HiddenMarkovModel (Bio::HMM::MarkovModel)   PairwiseAlignmentTests (test_Emboss)   Seq (Bio::Seq)   _MASTConsumer (Bio::Motif::Parsers::MEME)   
CompareAceParser (Bio::AlignAce::Parser)   HSExposureCA (Bio::PDB::HSExposure)   PalindromeCommandline (Bio::Emboss::Applications)   SeqFeature (Bio::SeqFeature)   _MASTConsumer (Bio::MEME::Parser)   
CompareAceParser (Bio::Motif::Parsers::AlignAce)   HSExposureCB (Bio::PDB::HSExposure)   Palindromic (Bio::Restriction::Restriction)   SeqFeatureCreation (test_SeqIO_features)   _MASTScanner (Bio::Motif::Parsers::MEME)   
CompareAceScanner (Bio::AlignAce::Scanner)   HSP (Bio::Blast::Record)   Parameters (Bio::Blast::Record)   SeqFeatureExtraction (test_SeqIO_features)   _MASTScanner (Bio::MEME::Parser)   
CompareAceScanner (Bio::Motif::Parsers::AlignAce)   
  I  
ParserFailureError (Bio::GenBank)   SeqInterfaceTest (test_BioSQL)   _MEMEConsumer (Bio::Motif::Parsers::MEME)   
ComparisonTestCase (run_tests)   identity_match (Bio::pairwise2)   ParsimonyTests (test_EmbossPhylipNew)   SeqMap (Bio::SCOP::Raf)   _MEMEConsumer (Bio::MEME::Parser)   
Connection (Bio::GFF)   IepCommandline (Bio::Emboss::Applications)   PatternHit (Bio::Prosite)   SeqMapIndex (Bio::SCOP::Raf)   _MEMEScanner (Bio::Motif::Parsers::MEME)   
Contig (Bio::Sequencing::Ace)   InDepthLoadTest (test_BioSQL)   PatternIO (Bio::NeuralNetwork::Gene::Pattern)   SeqMat (Bio::SubsMat)   _MEMEScanner (Bio::MEME::Parser)   
ConversionMutation (Bio::GA::Mutation::Simple)   Index (Bio::SCOP::Cla)   PatternIOTest (test_NNGene)   SeqmatchallCommandline (Bio::Emboss::Applications)   _Ncbiblast2SeqCommandline (Bio::Blast::Applications)   
ConversionTest (test_GAMutation)   IndexDictTests (test_SeqIO_index)   PatternRepository (Bio::NeuralNetwork::Gene::Pattern)   SeqRecord (Bio::SeqRecord)   _NcbiblastCommandline (Bio::Blast::Applications)   
ConvertTests (test_SeqIO_convert)   InputRecord (Bio::Emboss::PrimerSearch)   PatternRepositoryTest (test_NNGene)   SeqRecordCreation (test_SeqRecord)   _Option (Bio::Application)   
ConvertTests (test_AlignIO_convert)   InsdcScanner (Bio::GenBank::Scanner)   PDBIO (Bio::PDB::PDBIO)   SeqRecordMethods (test_SeqRecord)   _PPBuilder (Bio::PDB::Polypeptide)   
CreatePopulationTest (test_GAOrganism)   install_biopython (setup)   PDBList (Bio::PDB::PDBList)   SeqRetAlignIOTests (test_Emboss)   _RecordConsumer (Bio::PopGen::GenePop)   
ct (Bio::Sequencing::Ace)   Instance (Bio::MEME::Motif)   PDBParser (Bio::PDB::PDBParser)   SeqretCommandline (Bio::Emboss::Applications)   _RecordConsumer (Bio::GenBank)   
  D  
IntelliGeneticsDict (Bio::SeqIO::_index)   Pgdb_dbutils (BioSQL::DBUtils)   SeqRetSeqIOTests (test_Emboss)   _RecordConsumer (Bio::PopGen::FDist)   
DatabaseLoader (BioSQL::Loader)   Interaction (Bio::Pathway)   PhdDict (Bio::SeqIO::_index)   SequenceIterator (Bio::SeqIO::Interfaces)   _RecordConsumer (Bio::SwissProt::SProt)   
DatabaseRemover (BioSQL::Loader)   InterlacedSequenceIterator (Bio::SeqIO::Interfaces)   PhdWriter (Bio::SeqIO::PhdIO)   SequenceLine (Bio::UniGene)   _RecordConsumer (Bio::Prosite::Prodoc)   
DatabaseReport (Bio::Blast::Record)   InterleaveCrossover (Bio::GA::Crossover::GeneralPoint)   PhylipIterator (Bio::AlignIO::PhylipIO)   SequenceParser (Bio::Fasta)   _RecordConsumer (Bio::Prosite)   
DBSeqRecord (BioSQL::BioSeq)   InterleaveTest (test_GACrossover)   PhylipWriter (Bio::AlignIO::PhylipIO)   SequenceParser (Bio::SwissProt::SProt)   _RestrictedDict (Bio::SeqRecord)   
Defined (Bio::Restriction::Restriction)   InterProParser (Bio::InterPro)   PirDict (Bio::SeqIO::_index)   SequenceWriter (Bio::SeqIO::Interfaces)   _Scanner (Bio::Compass)   
Description (Bio::Blast::Record)   Iterator (Bio::GenBank)   Polypeptide (Bio::PDB::Polypeptide)   SequentialAlignmentWriter (Bio::AlignIO::Interfaces)   _Scanner (Bio::PopGen::GenePop)   
Diagram (Bio::Graphics::GenomeDiagram::_Diagram)   Iterator (Bio::Fasta)   PositionGap (Bio::SeqFeature)   SequentialSequenceWriter (Bio::SeqIO::Interfaces)   _Scanner (Bio::PopGen::FDist)   
DiagramTest (test_GenomeDiagram)   Iterator (Bio::Blast::NCBIStandalone)   PPBuilder (Bio::PDB::Polypeptide)   SGMLHandle (Bio::File)   _Scanner (Bio::Enzyme)   
DialignCommandline (Bio::Align::Applications::_Dialign)   Iterator (Bio::SCOP::Dom)   PrankCommandline (Bio::Align::Applications::_Prank)   SGMLStrippingConsumer (Bio::ParserSupport)   _Scanner (Bio::Blast::NCBIStandalone)   
Dictionary (Bio::SwissProt::SProt)   Iterator (Bio::Compass)   Primer3Commandline (Bio::Emboss::Applications)   ShortQueryBlastError (Bio::Blast::NCBIStandalone)   _Scanner (Bio::UniGene)   
Dictionary (Bio::Prosite::Prodoc)   IUPACAmbiguousDNA (Bio::Alphabet::IUPAC)   Primers (Bio::Emboss::Primer3)   SigilsTest (test_GenomeDiagram)   _Scanner (Bio::SwissProt::SProt)   
Dictionary (Bio::Prosite)   IUPACAmbiguousRNA (Bio::Alphabet::IUPAC)   PrimerSearchCommandline (Bio::Emboss::Applications)   SignatureCoder (Bio::NeuralNetwork::Gene::Signature)   _Scanner (Bio::Prosite::Prodoc)   
dictionary_match (Bio::pairwise2)   IUPACProtein (Bio::Alphabet::IUPAC)   PrimerSearchInputTest (test_EmbossPrimer)   SignatureCoderTest (test_NNGene)   _Scanner (Bio::Prosite)   
DifferentialCutsite (Bio::CAPS)   IUPACUnambiguousDNA (Bio::Alphabet::IUPAC)   PrintFormat (Bio::Restriction::PrintFormat)   SignatureFinder (Bio::NeuralNetwork::Gene::Signature)   _SequenceConsumer (Bio::SwissProt::SProt)   
DifferentialSchemaFitness (Bio::NeuralNetwork::Gene::Schema)   IUPACUnambiguousRNA (Bio::Alphabet::IUPAC)   ProbconsCommandline (Bio::Align::Applications::_Probcons)   SignatureFinderTest (test_NNGene)   _SequentialSeqFileDict (Bio::SeqIO::_index)   
DiffseqCommandline (Bio::Emboss::Applications)   
  K  
ProteinAnalysis (Bio::SeqUtils::ProtParam)   SimpleAlignTest (test_Muscle_tool)   _ShelveIndex (Bio::Index)   
DirectoryRetriever (Bio::PopGen::Async)   KDTree (Bio::KDTree::KDTree)   ProtsimLine (Bio::UniGene)   SimpleEnzyme (test_Restriction)   _Switch (Bio::Application)   
DisorderedAtom (Bio::PDB::Atom)   kNN (Bio::kNN)   PSIBlast (Bio::Blast::Record)   SimpleFinisher (Bio::NeuralNetwork::Gene::Schema)   _XMLparser (Bio::Blast::NCBIXML)   
DisorderedEntityWrapper (Bio::PDB::Entity)   KnownStateTrainer (Bio::HMM::Trainer)   PSIBlastParser (Bio::Blast::NCBIStandalone)   SinglePointCrossover (Bio::GA::Crossover::Point)   

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