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Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
Bio::PDB::HSExposure::_AbstractHSExposure
Bio::Application::_AbstractParameter
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::Compass::_Consumer
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::Motif::Parsers::MEME::_MASTConsumer
Bio::Motif::Parsers::MEME::_MASTScanner
Bio::Motif::Parsers::MEME::_MEMEConsumer
Bio::Motif::Parsers::MEME::_MEMEScanner
Bio::Blast::Applications::_Ncbiblast2SeqCommandline
Bio::Blast::Applications::_NcbiblastCommandline
Bio::Application::_Option
Bio::Blast::NCBIStandalone::_ParametersConsumer
BioSQL::DBUtils::_PostgreSQL_dbutils
Bio::PDB::Polypeptide::_PPBuilder
Bio::Blast::NCBIStandalone::_PSIBlastConsumer
Bio::PopGen::FDist::_RecordConsumer
Bio::Prosite::_RecordConsumer
Bio::Prosite::Prodoc::_RecordConsumer
Bio::UniGene::_RecordConsumer
Bio::Enzyme::_RecordConsumer
Bio::GenBank::_RecordConsumer
Bio::SeqRecord::_RestrictedDict
Bio::PopGen::FDist::_Scanner
Bio::Prosite::_Scanner
Bio::Prosite::Prodoc::_Scanner
Bio::Blast::NCBIStandalone::_Scanner
Bio::UniGene::_Scanner
Bio::Enzyme::_Scanner
Bio::Compass::_Scanner
Bio::Search::_SeqLength
Bio::Index::_ShelveIndex
Bio::Application::_Switch
Bio::Blast::NCBIXML::_XMLparser
test_PDB::A_ExceptionTest
Bio::GenBank::LocationParser::AbsoluteLocation
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::pairwise2::align
Bio::FSSP::fssp_rec::align
Bio::Motif::Applications::_AlignAce::AlignAceCommandline
Bio::Motif::Parsers::AlignAce::AlignAceConsumer
Bio::Motif::Parsers::AlignAce::AlignAceParser
Bio::Motif::Parsers::AlignAce::AlignAceScanner
Bio::Wise::psw::Alignment
Bio::Blast::Record::Alignment
Bio::Align::Generic::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::Phylo::PhyloXML::Annotation
Bio::GFF::GenericTools::AppendableListDictionary
Bio::Application::ApplicationError
Bio::Application::ApplicationResult
test_PopGen_DFDist::AppTest
test_PopGen_FDist::AppTest
test_PopGen_GenePop::AppTest
test_PopGen_GenePop_EasyController::AppTest
test_PopGen_SimCoal::AppTest
Bio::GFF::GenericTools::ArgsParser
Bio::SCOP::Astral
test_SCOP_Astral::AstralTests
Bio::PopGen::Async::Async
Bio::PDB::Atom::Atom
Bio::PDB::NeighborSearch::Atom
Bio::Graphics::Distribution::BarChartDistribution
test_GraphicsDistribution::BarChartTest
Bio::NeuralNetwork::BackPropagation::Network::BasicNetwork
Bio::HMM::Trainer::BaumWelchTrainer
Bio::SeqFeature::BeforePosition
Bio::GenBank::LocationParser::Between
Bio::SeqFeature::BetweenPosition
Bio::Phylo::PhyloXML::BinaryCharacters
Bio::BiopythonDeprecationWarning
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::Sequencing::Ace::bs
setup::build_ext_biopython
setup::build_py_biopython
Bio::PDB::Polypeptide::CaPPBuilder
Bio::CAPS::CAPSMap
Bio::Affy::CelFile::CelConsumer
Bio::Affy::CelFile::CelParser
Bio::Affy::CelFile::CelRecord
Bio::Affy::CelFile::CelScanner
Bio::Crystal::Chain
Bio::Nexus::Nodes::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::Clustalw::ClustalAlignment
Bio::AlignIO::ClustalIO::ClustalIterator
Bio::Align::Applications::_Clustalw::ClustalwCommandline
Bio::AlignIO::ClustalIO::ClustalWriter
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
Bio::Graphics::Comparative::ComparativeScatterPlot
test_GraphicsBitmaps::ComparativeTest
test_GraphicsGeneral::ComparativeTest
Bio::Motif::Applications::_AlignAce::CompareAceCommandline
Bio::Motif::Parsers::AlignAce::CompareAceConsumer
Bio::Motif::Parsers::AlignAce::CompareAceParser
Bio::Motif::Parsers::AlignAce::CompareAceScanner
run_tests::ComparisonTestCase
test_Compass::CompassTest
Bio::Phylo::PhyloXML::Confidence
Bio::GFF::Connection
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
Bio::Entrez::Parser::CorruptedXMLError
Bio::DocSQL::Create
Bio::PropertyManager::CreateDict
test_GAOrganism::CreatePopulationTest
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::Enzyme::DataRecord
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::Prosite::Dictionary
Bio::Prosite::Prodoc::Dictionary
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
Bio::Emboss::Applications::EConsenseCommandline
test_Entrez::EFetchTest
test_Entrez::EGQueryTest
test_Entrez::EInfoTest
Bio::Emboss::Applications::EInvertedCommandline
test_Entrez::ELinkTest
Bio::SeqIO::_index::EmblDict
Bio::GenBank::Scanner::EmblScanner
Bio::SeqIO::InsdcIO::EmblWriter
Bio::AlignIO::EmbossIO::EmbossIterator
Bio::AlignIO::EmbossIO::EmbossWriter
Bio::Emboss::Applications::ENeighborCommandline
Bio::PDB::Entity::Entity
test_SeqIO_online::EntrezTests
test_Restriction::EnzymeComparison
Bio::Enzyme::EnzymeRecord
test_Entrez::EPostTest
Bio::Emboss::Applications::EProtDistCommandline
Bio::Emboss::Applications::EProtParsCommandline
test_Entrez::ESearchTest
Bio::Emboss::Applications::ESeqBootCommandline
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::AlignIO::FastaIO::FastaM10Iterator
Bio::SeqIO::FastaIO::FastaWriter
Bio::SeqIO::_index::FastqDict
Bio::SeqIO::QualityIO::FastqIlluminaWriter
Bio::SeqIO::QualityIO::FastqPhredWriter
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::GFF::Feature
Bio::Graphics::GenomeDiagram::_Feature::Feature
Bio::GFF::FeatureAggregate
Bio::GFF::easy::FeatureDict
Bio::SeqFeature::FeatureLocation
Bio::GenBank::LocationParser::FeatureName
Bio::GenBank::FeatureParser
Bio::GFF::FeatureQuery
Bio::GFF::FeatureQueryRow
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::GFF::GenericTools::ForgivingDictionary
Bio::Restriction::Restriction::FormattedSeq
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 idoerg@cc.huji.ac.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::GenBank::LocationParser::Function
Bio::Emboss::Applications::FuzznucCommandline
Bio::Alphabet::Gapped
Bio::SeqIO::_index::GenBankDict
Bio::GenBank::Scanner::GenBankScanner
Bio::SeqIO::InsdcIO::GenBankWriter
Bio::PopGen::GenePop::Controller::GenePopController
Bio::GA::Crossover::GeneralPoint::GeneralPointCrossover
Bio::GA::Evolver::GenerationEvolver
BioSQL::DBUtils::Generic_dbutils
Bio::Parsers::spark::GenericASTBuilder
Bio::Parsers::spark::GenericASTMatcher
Bio::Parsers::spark::GenericASTTraversal
Bio::Parsers::spark::GenericASTTraversalPruningException
Bio::Parsers::spark::GenericParser
Bio::Parsers::spark::GenericScanner
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
test_Pathway::HashSetTestCase
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::GenBank::LocationParser::HighBound
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::GenBank::LocationParser::Integer
Bio::Entrez::Parser::IntegerElement
Bio::SeqIO::_index::IntelliGeneticsDict
Bio::Pathway::Interaction
Bio::SeqIO::Interfaces::InterlacedSequenceIterator
Bio::GA::Crossover::GeneralPoint::InterleaveCrossover
test_GACrossover::InterleaveTest
Bio::InterPro::InterProParser
test_Phylo::IOTests
Bio::SeqUtils::IsoelectricPoint::IsoelectricPoint
Bio::DocSQL::IterationCursor
Bio::Blast::NCBIStandalone::Iterator
Bio::UniGene::Iterator
Bio::Enzyme::Iterator
Bio::GenBank::Iterator
Bio::Compass::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::GFF::easy::Location
Bio::GFF::easy::LocationFromCoords
Bio::GFF::easy::LocationFromString
Bio::GFF::easy::LocationJoin
Bio::GenBank::LocationParser::LocationParser
Bio::GenBank::LocationParserError
Bio::GenBank::LocationParser::LocationScanner
Bio::HMM::DynamicProgramming::LogDPAlgorithms
Bio::LogisticRegression::LogisticRegression
Bio::SubsMat::LogOddsMatrix
Bio::GenBank::LocationParser::LowBound
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::Motif::Parsers::MEME::MASTParser
Bio::Motif::Parsers::MEME::MASTRecord
Bio::MaxEntropy::MaxEntropy
Bio::Motif::Parsers::MEME::MEMEInstance
Bio::Motif::Parsers::MEME::MEMEMotif
Bio::Motif::Parsers::MEME::MEMEParser
Bio::Motif::Parsers::MEME::MEMERecord
Bio::GFF::binning::Meta
Bio::Restriction::Restriction::Meth_Dep
Bio::Restriction::Restriction::Meth_Undep
test_PhyloXML::MethodTests
Bio::MissingExternalDependencyError
Bio::MissingPythonDependencyError
Bio::SeqUtils::MissingTable
nextorf::MissingTable
test_Phylo::MixinTests
Bio::PDB::MMCIF2Dict::MMCIF2Dict
Bio::PDB::MMCIFParser::MMCIFParser
Bio::PDB::Model::Model
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::Clustalw::MultipleAlignCL
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::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::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
Bio::Restriction::Restriction::OneCut
Bio::SeqFeature::OneOfPosition
Bio::Graphics::BasicChromosome::Organism
Bio::GA::Organism::Organism
test_GraphicsChromosome::OrganismGraphicTest
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::Blast::Record::Parameters
SeqGui::ParamsPanel
Bio::SeqIO::UniprotIO::Parser
Bio::ExPASy::ScanProsite::Parser
Bio::Phylo::NewickIO::Parser
Bio::Phylo::PhyloXMLIO::Parser
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::GenBank::LocationParser::Path
Bio::Prosite::PatternHit
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::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::PropertyManager::PropertyManager
Bio::Prosite::Pattern::Prosite
Bio::Prosite::Pattern::PrositeAlphabet
Bio::Prosite::Pattern::PrositeMatch
Bio::Prosite::Pattern::PrositeTerm
Bio::Alphabet::ProteinAlphabetProtein
Bio::SeqUtils::ProtParam::ProteinAnalysis
Bio::Phylo::PhyloXML::ProteinDomain
Bio::SeqUtils::ProteinXProtein
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::DocSQL::Query
Bio::Search::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::GenBank::LocationParser::Range
Bio::Sequencing::Ace::rd
Bio::Pathway::Reaction
test_Pathway::ReactionTestCase
Bio::Sequencing::Ace::Reads
test_BioSQL::ReadTest
Bio::Restriction::_Update::Update::RebaseUpdate
Bio::PopGen::GenePop::Record
Bio::GenBank::Record::Record
Bio::PopGen::GenePop::LargeFileParser::Record
Bio::Prosite::Record
Bio::Prosite::Prodoc::Record
Bio::Affy::CelFile::Record
Bio::SCOP::Hie::Record
Bio::SCOP::Cla::Record
Bio::ExPASy::Enzyme::Record
Bio::KEGG::Compound::Record
Bio::SwissProt::Record
Bio::SwissProt::KeyWList::Record
Bio::Medline::Record
Bio::UniGene::Record
Bio::Motif::Parsers::AlignAce::Record
Bio::Motif::Parsers::MAST::Record
Bio::Emboss::Primer3::Record
Bio::Sequencing::Phd::Record
Bio::Geo::Record::Record
Bio::ExPASy::ScanProsite::Record
Bio::KEGG::Enzyme::Record
Bio::ExPASy::Prodoc::Record
Bio::ExPASy::Prosite::Record
Bio::InterPro::Record
Bio::Compass::Record
Bio::SCOP::Des::Record
Bio::Cluster::Record
Bio::SCOP::Dom::Record
Bio::PopGen::FDist::Record
Bio::PopGen::FDist::RecordParser
Bio::UniGene::RecordParser
Bio::Prosite::RecordParser
Bio::Prosite::Prodoc::RecordParser
Bio::Enzyme::RecordParser
Bio::GenBank::RecordParser
Bio::Compass::RecordParser
test_PopGen_FDist_nodepend::RecordTest
test_PopGen_GenePop_nodepend::RecordTest
Bio::GenBank::Record::Reference
Bio::Prosite::Prodoc::Reference
Bio::ExPASy::Prodoc::Reference
Bio::Phylo::PhyloXML::Reference
Bio::SeqFeature::Reference
Bio::SwissProt::Reference
Region
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::GFF::RetrieveSeqname
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_GAMutation::SafeFitnessTest
test_GACrossover::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_Scop::ScopTests
Bio::Motif::Thresholds::ScoreDistribution
Bio::Search::Search
Bio::Alphabet::SecondaryStructureOther per-sequence encodings
Bio::GFF::Segment
Bio::PDB::PDBIO::Select
Bio::Seq::Seq
Bio::SeqFeature::SeqFeature
test_SeqIO_features::SeqFeatureCreation
test_SeqIO_features::SeqFeatureExtractionWritingReading
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::SeqIO::_index::SequentialSeqFileDict
Bio::SeqIO::Interfaces::SequentialSequenceWriter
Bio::SeqIO::_index::SffDict
Bio::SeqIO::_index::SffTrimmedDict
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::Cache::SimCoalCache
Bio::PopGen::SimCoal::Async::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::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::Entrez::Parser::StringElement
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::GFF::GenericTools::Surrogate
Bio::GFF::GenericTools::SurrogateNotInitedError
Bio::SVDSuperimposer::SVDSuperimposer::SVDSuperimposer
Bio::SeqIO::_index::SwissDict
Bio::GenBank::LocationParser::Symbol
Bio::Pathway::System
Bio::SeqIO::_index::TabDict
Bio::Search::TableInfo
Bio::SeqIO::TabIO::TabWriter
Bio::ParserSupport::TaggingConsumer
Bio::Phylo::PhyloXML::Taxonomy
test_TCoffee_tool::TCoffeeApplication
Bio::Align::Applications::_TCoffee::TCoffeeCommandline
Bio::Graphics::BasicChromosome::TelomereSegment
Bio::GFF::GenericTools::TempFile
test_PopGen_SimCoal_nodepend::TemplateTest
setup::test_biopython
test_lowess::test_lowess
test_GAOrganism::TestAlphabet
test_GASelection::TestAlphabet
test_GACrossover::TestAlphabet
test_GARepair::TestAlphabet
test_GAMutation::TestAlphabet
test_NCBITextParser::TestBlastRecord
test_CAPS::TestCAPS
test_Cluster::TestCluster
test_GACrossover::TestCrossover
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_prosite_patterns::TestPrositePattern
test_prosite2::TestPrositeRead
test_prosite1::TestPrositeRead
test_psw::TestPSW
test_SeqIO_QualityIO::TestQual
test_SeqIO_QualityIO::TestReadWrite
test_SeqIO_QualityIO::TestReferenceFastqConversions
test_SeqIO_QualityIO::TestReferenceSffConversions
run_tests::TestRunner
test_SwissProt::TestSwissProt
test_trie::TestTrie
test_trie::TestTrieFind
test_UniGene::TestUniGene
test_Uniprot::TestUniprot
test_Wise::TestWise
test_Wise::TestWiseDryRun
test_SeqIO_features::TestWriteRead
test_SeqIO_QualityIO::TestWriteRead
Bio::Alphabet::ThreeLetterProtein
test_SeqIO_FastaIO::TitleFunctions
Bio::GenBank::LocationParser::Token
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
Bio::Transcribe::Transcribe
test_BioSQL::TransferTest
Transition
Bio::Data::CodonTable::TranslationError
test_Emboss::TranslationTests
Bio::Translate::Translator
Bio::Nexus::Trees::Tree
Bio::Phylo::BaseTree::Tree
Bio::Phylo::Newick::Tree
test_EmbossPhylipNew::TreeComparisonTests
Bio::Phylo::BaseTree::TreeElement
Bio::Nexus::Trees::TreeError
Bio::Phylo::BaseTree::TreeMixin
test_PhyloXML::TreeTests
test_Phylo::TreeTests
Trie
trieobject
Bio::GenBank::LocationParser::TwoBound
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::UniGene::UnigeneProtsimRecord
Bio::UniGene::UnigeneRecord
Bio::UniGene::UnigeneSequenceRecord
Bio::UniGene::UnigeneSTSRecord
Bio::SeqIO::_index::UniprotDict
Bio::Restriction::Restriction::Unknown
Bio::SeqFeature::UnknownPosition
Bio::Seq::UnknownSeq
Bio::GenBank::LocationParser::UnsignedInteger
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::GFF::GenericTools::VerboseDict
Bio::GFF::GenericTools::VerboseList
Bio::Sequencing::Ace::wa
Bio::Emboss::Applications::WaterCommandline
Bio::SeqFeature::WithinPosition
Bio::Sequencing::Ace::wr
Bio::Phylo::PhyloXMLIO::Writer
Bio::Phylo::NewickIO::Writer
test_PhyloXML::WriterTests
xbb_sequence::xbb_sequence
xbb_translations::xbb_translations
xbb_widget::xbb_widget
xbb_help::xbbtools_help
xbb_search::XDNAsearch
Bio::NMR::xpktools::XpkEntry
yy_buffer_state

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