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Bio.Crystal.Chain
Bio.Seq.MutableSeq
Bio.Seq.Seq
Martel.Expression.Expression
Martel.Expression.NullOp
Martel.Expression.Seq
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__builtin__.str
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Bio.EUtils.Datatypes.Expression
object
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__builtin__.type
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Bio.Affy.CelFile.CelParser
Bio.Decode.FunctionCall
Bio.Decode.FunctionCallChain
Bio.EUtils.parse.GetObject
Bio.config._support.make_rate_limited_function
Bio.config._support.make_timed_function
Bio.pairwise2.affine_penalty
Bio.pairwise2.dictionary_match
Bio.pairwise2.identity_match
Martel.Dispatch.MulticallEnd
Martel.Dispatch.MulticallStart
Martel.Dispatch.RemapEnd
Martel.Dispatch.RemapStart
Martel.Generate.CheckAssert
Martel.Generate.CheckAssertNot
Martel.Generate.CheckGroupRef
Martel.Generate.SetGroupValue
Martel.Generate._call_call
Martel.Generate._call_calltag
Martel.Generate.print_debug
Martel.Generate.print_info
type
__cmp__
Bio.Alphabet.HasStopCodon
Bio.Decode.Token
Bio.Decode.ValueToken
Bio.GA.Organism.Organism
Bio.SeqFeature.AbstractPosition
__builtin__.dict
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Bio.EUtils.MultiDict._BaseMultiDict
Bio.Pathway.Rep.HashSet.HashSet
Martel.LAX._IsIn
xml.sax.xmlreader.AttributesImpl
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Bio.Index._InMemoryIndex
Bio.Index._ShelveIndex
Bio.Mindy.FlatDB.MemoryFlatDB
Bio.MultiProc.Task.Task
Bio.MultiProc.copen._ProcHandle
__del_annotations
BioSQL.BioSeq.DBSeqRecord
__del_dbxrefs
__del_features
__del_seq
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Bio.EUtils.POM.ElementNode
__builtin__.object
exceptions.BaseException
__delitem__
Bio.Crystal.Crystal
Bio.EUtils.MultiDict.OrderedMultiDict
Bio.EUtils.MultiDict.UnorderedMultiDict
Martel.msre_parse.SubPattern
__delslice__
__dictoffset__
__eq__
Bio.Crystal.Hetero
Bio.EUtils.Datatypes.CheckLinkSet
Bio.EUtils.Datatypes.DBIds
Bio.EUtils.Datatypes.Date
Bio.EUtils.Datatypes.IdCheck
Bio.EUtils.Datatypes.IdUrlSet
Bio.EUtils.Datatypes.Link
Bio.EUtils.Datatypes.LinkSetDb
Bio.EUtils.Datatypes.LinksLinkSet
Bio.EUtils.Datatypes.NeighborLinkSet
Bio.EUtils.Datatypes.ObjUrl
Bio.EUtils.Datatypes.Problem
Bio.EUtils.Datatypes.Provider
Bio.Pathway.Reaction
Bio.Pathway.Rep.Graph.Graph
Bio.Pathway.Rep.MultiGraph.MultiGraph
__flags__
__ge__
__get_annotations
__get_dbxrefs
__get_features
__get_seq
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Bio.Alphabet.AlphabetEncoder
Bio.Data.CodonTable.AmbiguousCodonTable
Bio.File.SGMLHandle
Bio.File.UndoHandle
Bio.FilteredReader.FilteredReader
Bio.Gobase.Dictionary
Bio.Mindy.Location.Location
Bio.MultiProc.copen._PickleHandle
Bio.ParserSupport.AbstractConsumer
Bio.ParserSupport.SGMLStrippingConsumer
Bio.ParserSupport.TaggingConsumer
Bio.Prosite.Dictionary
Bio.Prosite.Pattern.Prosite
Bio.Prosite.Prodoc.Dictionary
Bio.Rebase.Dictionary
Bio.SGMLExtractor.SGMLExtractorHandle
Bio.Search._SeqLength
Bio.SeqFeature.FeatureLocation
Bio.SwissProt.SProt.Dictionary
Martel.LAX.LAX
__getattribute__
__getitem__
Bio.Align.AlignInfo.PSSM
Bio.DBXRef.BioformatDBName
Bio.DBXRef.UnknownDBName
Bio.Data.CodonTable.AmbiguousForwardTable
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet
Bio.EUtils.HistoryClient.BaseHistoryRecordSet
Bio.FSSP.fssp_rec.fff_rec
Bio.FormatIO.FormatIOIterator
Bio.Mindy.BaseDB.DictLookup
Bio.Mindy.BaseDB.OpenDB
Bio.Mindy.FlatDB.BisectFile
Bio.Mindy.FlatDB.DiskFlatDB
Bio.Mindy.FlatDB.PrimaryNamespace
Bio.Mindy.FlatDB.PrimaryTable
Bio.Mindy.FlatDB.SecondaryNamespace
Bio.Mindy.FlatDB.SecondaryTable
Bio.PropertyManager.CreateDict
Bio.Prosite.ExPASyDictionary
Bio.Prosite.Pattern.PrositeMatch
Bio.Prosite.Prodoc.ExPASyDictionary
Bio.PubMed.Dictionary
Bio.SeqIO.FASTA.FastaReader
Bio.SeqIO.generic.GenericFormat
Bio.SwissProt.SProt.ExPASyDictionary
Bio.config.DBRegistry.DBGroup
Bio.config.DBRegistry.DBObject
Bio.config.Registry.Registry
Bio.config.SeqDBRegistry.SeqDBRegistry
BioSQL.BioSeq.DBSeq
BioSQL.BioSeqDatabase.BioSeqDatabase
BioSQL.BioSeqDatabase.DBServer
Martel.Iterator.Iterate
Martel.Parser.MartelAttributeList
Martel.test.support.Storage
xml.sax._exceptions.SAXException
__getnewargs__
__getslice__
__gt__
__hash__
Bio.Pathway.Interaction
__iadd__
Martel.Parser.ParserIncompleteException
Martel.Parser.ParserPositionException
__imul__
__init_
__init__
Bio.Affy.CelFile.CelConsumer
Bio.Affy.CelFile.CelRecord
Bio.Ais.Immune
Bio.Ais.Lymphocyte
Bio.Align.AlignInfo.SummaryInfo
Bio.Align.FormatConvert.FormatConverter
Bio.Align.Generic.Alignment
Bio.AlignAce.Applications.AlignAceCommandline
Bio.AlignAce.Applications.CompareAceCommandline
Bio.AlignAce.Motif.Motif
Bio.AlignAce.Parser.AlignAceConsumer
Bio.AlignAce.Parser.AlignAceParser
Bio.AlignAce.Parser.CompareAceConsumer
Bio.AlignAce.Parser.CompareAceParser
Bio.Alphabet.Gapped
Bio.Application.AbstractCommandline
Bio.Application.ApplicationResult
Bio.Application._AbstractParameter
Bio.Blast.Applications.BlastallCommandline
Bio.Blast.Applications.FastacmdCommandline
Bio.Blast.NCBIStandalone.BlastErrorParser
Bio.Blast.NCBIStandalone.BlastParser
Bio.Blast.NCBIStandalone.Iterator
Bio.Blast.NCBIStandalone.PSIBlastParser
Bio.Blast.NCBIStandalone._BlastConsumer
Bio.Blast.NCBIStandalone._BlastErrorConsumer
Bio.Blast.NCBIStandalone._PSIBlastConsumer
Bio.Blast.NCBIWWW.BlastParser
Bio.Blast.NCBIWWW._FormParser
Bio.Blast.NCBIXML.BlastParser
Bio.Blast.NCBIXML._XMLparser
Bio.Blast.ParseBlastTable.BlastTableEntry
Bio.Blast.ParseBlastTable.BlastTableReader
Bio.Blast.ParseBlastTable.BlastTableRec
Bio.Blast.Record.Alignment
Bio.Blast.Record.Blast
Bio.Blast.Record.DatabaseReport
Bio.Blast.Record.Description
Bio.Blast.Record.HSP
Bio.Blast.Record.Header
Bio.Blast.Record.MultipleAlignment
Bio.Blast.Record.PSIBlast
Bio.Blast.Record.Parameters
Bio.Blast.Record.Round
Bio.CAPS.CAPSMap
Bio.CAPS.DifferentialCutsite
Bio.Compass.Iterator
Bio.Compass.Record
Bio.Compass.RecordParser
Bio.Compass._Consumer
Bio.Crystal.CrystalError
Bio.Crystal.Error
Bio.DBXRef.DBXRef
Bio.Data.CodonTable.CodonTable
Bio.Data.CodonTable.NCBICodonTable
Bio.Decode.DecodeParser
Bio.Decode.DecodeScanner
Bio.Decode.Float
Bio.Decode.Function
Bio.Decode.FunctionName
Bio.Decode.Integer
Bio.Decode.String
Bio.EUtils.Config.DatabaseInfo
Bio.EUtils.DBIdsClient.DBIdsClient
Bio.EUtils.DBIdsClient.DBIdsLookup
Bio.EUtils.Datatypes.BinaryOp
Bio.EUtils.Datatypes.DateRange
Bio.EUtils.Datatypes.EUtilsSearchError
Bio.EUtils.Datatypes.PostResult
Bio.EUtils.Datatypes.Range
Bio.EUtils.Datatypes.SearchResult
Bio.EUtils.Datatypes.Summary
Bio.EUtils.Datatypes.Term
Bio.EUtils.Datatypes.WithinNDays
Bio.EUtils.HistoryClient.HistoryClient
Bio.EUtils.HistoryClient.HistoryCookie
Bio.EUtils.HistoryClient.HistoryLookup
Bio.EUtils.HistoryClient.HistoryRecord
Bio.EUtils.POM.Comment
Bio.EUtils.POM.ContentModel
Bio.EUtils.POM.DTDConsumerForSourceGeneration
Bio.EUtils.POM.IndentedText
Bio.EUtils.POM.ObjectParserHandler
Bio.EUtils.POM.POMDocument
Bio.EUtils.POM.XMLAttribute
Bio.EUtils.POM._ContentModelGenerator
Bio.EUtils.ReseekFile.ReseekFile
Bio.EUtils.ThinClient.ThinClient
Bio.EUtils.parse.UsePOMParser
Bio.EUtils.sourcegen.ClassHolder
Bio.EUtils.sourcegen.FunctionHolder
Bio.EUtils.sourcegen.MethodHolder
Bio.EUtils.sourcegen.SourceFile
Bio.EUtils.sourcegen.SourceGen
Bio.Emboss.Applications.EConsenseCommandline
Bio.Emboss.Applications.EInvertedCommandline
Bio.Emboss.Applications.ENeighborCommandline
Bio.Emboss.Applications.EProtDistCommandline
Bio.Emboss.Applications.EProtParsCommandline
Bio.Emboss.Applications.ESeqBootCommandline
Bio.Emboss.Applications.ETandemCommandline
Bio.Emboss.Applications.Est2GenomeCommandline
Bio.Emboss.Applications.FuzznucCommandline
Bio.Emboss.Applications.PalindromeCommandline
Bio.Emboss.Applications.Primer3Commandline
Bio.Emboss.Applications.PrimerSearchCommandline
Bio.Emboss.Applications.TranalignCommandline
Bio.Emboss.Applications.WaterCommandline
Bio.Emboss.Primer.Primer3Parser
Bio.Emboss.Primer.Primer3Primers
Bio.Emboss.Primer.Primer3Record
Bio.Emboss.Primer.PrimerSearchAmplifier
Bio.Emboss.Primer.PrimerSearchInputRecord
Bio.Emboss.Primer.PrimerSearchOutputRecord
Bio.Emboss.Primer.PrimerSearchParser
Bio.Emboss.Primer._Primer3RecordConsumer
Bio.Emboss.Primer._Primer3Scanner
Bio.Emboss.Primer._PrimerSearchRecordConsumer
Bio.Emboss.Primer._PrimerSearchScanner
Bio.Enzyme.DataRecord
Bio.Enzyme.EnzymeRecord
Bio.Enzyme.Iterator
Bio.Enzyme.RecordParser
Bio.Enzyme._RecordConsumer
Bio.FSSP.FSSPAlignDict
Bio.FSSP.FSSPAlignRec
Bio.FSSP.FSSPHeader
Bio.FSSP.FSSPSumRec
Bio.FSSP.FSSPTools.FSSPMultAlign
Bio.FSSP.PosAlign
Bio.File.MyParser
Bio.File.SGMLStripper
Bio.FormatIO.FormatIO
Bio.GA.Crossover.General.SafeFitnessCrossover
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover
Bio.GA.Crossover.Point.SinglePointCrossover
Bio.GA.Crossover.TwoPoint.TwoPointCrossover
Bio.GA.Crossover.Uniform.UniformCrossover
Bio.GA.Evolver.GenerationEvolver
Bio.GA.Evolver.SteadyStateEvolver
Bio.GA.Mutation.General.SafeFitnessMutation
Bio.GA.Mutation.Simple.ConversionMutation
Bio.GA.Mutation.Simple.SinglePositionMutation
Bio.GA.Repair.Stabilizing.AmbiguousRepair
Bio.GA.Selection.Abstract.AbstractSelection
Bio.GA.Selection.Diversity.DiversitySelection
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection
Bio.GA.Selection.Tournament.TournamentSelection
Bio.Gobase.GeneRecord
Bio.Gobase.Iterator
Bio.Gobase.ProteinRecord
Bio.Gobase.Record
Bio.Gobase.RecordParser
Bio.Gobase.SequenceRecord
Bio.Gobase._RecordConsumer
Bio.Graphics.BasicChromosome.Chromosome
Bio.Graphics.BasicChromosome.ChromosomeSegment
Bio.Graphics.BasicChromosome.Organism
Bio.Graphics.BasicChromosome.TelomereSegment
Bio.Graphics.BasicChromosome._ChromosomeComponent
Bio.Graphics.Comparative.ComparativeScatterPlot
Bio.Graphics.DisplayRepresentation.ChromosomeCounts
Bio.Graphics.Distribution.BarChartDistribution
Bio.Graphics.Distribution.DistributionPage
Bio.Graphics.Distribution.LineDistribution
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
Bio.HMM.DynamicProgramming.LogDPAlgorithms
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
Bio.HMM.MarkovModel.HiddenMarkovModel
Bio.HMM.MarkovModel.MarkovModelBuilder
Bio.HMM.Trainer.AbstractTrainer
Bio.HMM.Trainer.BaumWelchTrainer
Bio.HMM.Trainer.KnownStateTrainer
Bio.HMM.Trainer.TrainingSequence
Bio.HotRand.HotCache
Bio.HotRand.HotRandom
Bio.LogisticRegression.LogisticRegression
Bio.MEME.Motif.Instance
Bio.MEME.Motif.MEMEMotif
Bio.MEME.Motif.Motif
Bio.MEME.Parser.MASTParser
Bio.MEME.Parser.MASTRecord
Bio.MEME.Parser.MEMEParser
Bio.MEME.Parser.MEMERecord
Bio.MEME.Parser._MASTConsumer
Bio.MEME.Parser._MEMEConsumer
Bio.MarkovModel.MarkovModel
Bio.MarkupEditor.MarkupEditor
Bio.MarkupEditor.MidPoint
Bio.MaxEntropy.MaxEntropy
Bio.Medline.Iterator
Bio.Medline.NLMMedlineXML.CitationParser
Bio.Medline.NLMMedlineXML._IndexerHandler
Bio.Medline.NLMMedlineXML._SavedDataHandle
Bio.Medline.Record
Bio.Medline.RecordParser
Bio.Medline._RecordConsumer
Bio.Mindy.FlatDB.BaseFlatDB
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder
Bio.Mindy.SimpleSeqRecord.FunctionIndexer
Bio.Mindy.SimpleSeqRecord.SimpleIndexer
Bio.Mindy.XPath.GrabXPathNodes
Bio.MultiProc.Scheduler.Scheduler
Bio.NMR.xpktools.Peaklist
Bio.NMR.xpktools.XpkEntry
Bio.NaiveBayes.NaiveBayes
Bio.Ndb.Record
Bio.NetCatch.ExtractUrls
Bio.NetCatch.NetCatch
Bio.NetCatch.Url
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
Bio.NeuralNetwork.Gene.Motif.MotifCoder
Bio.NeuralNetwork.Gene.Motif.MotifFinder
Bio.NeuralNetwork.Gene.Pattern.PatternIO
Bio.NeuralNetwork.Gene.Pattern.PatternRepository
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator
Bio.NeuralNetwork.Gene.Schema.Schema
Bio.NeuralNetwork.Gene.Schema.SchemaCoder
Bio.NeuralNetwork.Gene.Schema.SchemaFactory
Bio.NeuralNetwork.Gene.Schema.SchemaFinder
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher
Bio.NeuralNetwork.Gene.Signature.SignatureCoder
Bio.NeuralNetwork.Gene.Signature.SignatureFinder
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop
Bio.NeuralNetwork.Training.ExampleManager
Bio.NeuralNetwork.Training.TrainingExample
Bio.Nexus.Nexus.Block
Bio.Nexus.Nexus.CharBuffer
Bio.Nexus.Nexus.Commandline
Bio.Nexus.Nexus.Nexus
Bio.Nexus.Nexus.StepMatrix
Bio.Nexus.Nodes.Chain
Bio.Nexus.Nodes.Node
Bio.Nexus.Trees.NodeData
Bio.Nexus.Trees.Tree
Bio.ParserSupport.EventGenerator
Bio.Parsers.spark.GenericASTBuilder
Bio.Parsers.spark.GenericASTMatcher
Bio.Parsers.spark.GenericASTTraversal
Bio.Parsers.spark.GenericParser
Bio.Parsers.spark.GenericScanner
Bio.Pathway.Network
Bio.Pathway.System
Bio.PropertyManager.PropertyManager
Bio.Prosite.Iterator
Bio.Prosite.Pattern.PrositeTerm
Bio.Prosite.PatternHit
Bio.Prosite.Prodoc.Iterator
Bio.Prosite.Prodoc.Record
Bio.Prosite.Prodoc.RecordParser
Bio.Prosite.Prodoc.Reference
Bio.Prosite.Prodoc._RecordConsumer
Bio.Prosite.Record
Bio.Prosite.RecordParser
Bio.Prosite._RecordConsumer
Bio.Rebase.Iterator
Bio.Rebase.Record
Bio.Rebase.RecordParser
Bio.Rebase._RecordConsumer
Bio.SGMLExtractor.LocalParser
Bio.SGMLExtractor.SGMLExtractor
Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
Bio.Search.Algorithm
Bio.Search.Database
Bio.Search.HSP
Bio.Search.HSPSeq
Bio.Search.Hit
Bio.Search.HomologySeq
Bio.Search.Query
Bio.Search.Search
Bio.Search.TableInfo
Bio.SeqFeature.AfterPosition
Bio.SeqFeature.BeforePosition
Bio.SeqFeature.BetweenPosition
Bio.SeqFeature.ExactPosition
Bio.SeqFeature.OneOfPosition
Bio.SeqFeature.PositionGap
Bio.SeqFeature.Reference
Bio.SeqFeature.SeqFeature
Bio.SeqFeature.WithinPosition
Bio.SeqIO.FASTA.FastaWriter
Bio.SeqIO.generic.ClustalFormat
Bio.SeqIO.generic.EMBLFormat
Bio.SeqIO.generic.FastaFormat
Bio.SeqIO.generic.GCGFormat
Bio.SeqIO.generic.LargeFastaFormat
Bio.SeqIO.generic.NexusFormat
Bio.SeqIO.generic.PirFormat
Bio.SeqIO.generic.ReadSeq
Bio.SeqIO.generic.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.Sequencing.Ace.ACEFileRecord
Bio.Sequencing.Ace.ACEParser
Bio.Sequencing.Ace.Contig
Bio.Sequencing.Ace.Iterator
Bio.Sequencing.Ace.Reads
Bio.Sequencing.Ace.RecordParser
Bio.Sequencing.Ace._RecordConsumer
Bio.Sequencing.Ace.af
Bio.Sequencing.Ace.bs
Bio.Sequencing.Ace.ct
Bio.Sequencing.Ace.ds
Bio.Sequencing.Ace.qa
Bio.Sequencing.Ace.rd
Bio.Sequencing.Ace.rt
Bio.Sequencing.Ace.wa
Bio.Sequencing.Ace.wr
Bio.Sequencing.Phd.Iterator
Bio.Sequencing.Phd.Record
Bio.Sequencing.Phd.RecordParser
Bio.Sequencing.Phd._RecordConsumer
Bio.StdHandler.ConvertDispatchHandler
Bio.StdHandler.ConvertHandler
Bio.StdHandler.Feature
Bio.StdHandler.Handle_dbxref
Bio.StdHandler.Handle_feature_location
Bio.StdHandler.Handle_feature_qualifier
Bio.StdHandler.Handle_features
Bio.StdHandler.Handle_hsp
Bio.StdHandler.RecognizeHandler
Bio.SubsMat.FreqTable.FreqTable
Bio.SubsMat.SeqMat
Bio.SwissProt.KeyWList.ListParser
Bio.SwissProt.KeyWList._ListConsumer
Bio.SwissProt.SProt.Iterator
Bio.SwissProt.SProt.Record
Bio.SwissProt.SProt.RecordParser
Bio.SwissProt.SProt.Reference
Bio.SwissProt.SProt.SequenceParser
Bio.SwissProt.SProt._RecordConsumer
Bio.SwissProt.SProt._SequenceConsumer
Bio.Transcribe.Transcribe
Bio.Translate.Translator
Bio.UniGene.Record
Bio.WWW.RequestLimiter
Bio.Wise.psw.AlignmentColumn
Bio.Wise.psw.ColumnUnit
Bio.Writer.Writer
Bio.builders.Search.search.BuildSearch
Bio.builders.SeqRecord.sequence.BuildSeqRecord
Bio.config.DBRegistry.BioCorbaDB
Bio.config.DBRegistry.BioSQLDB
Bio.config.DBRegistry.CGIDB
Bio.config.DBRegistry.DBRegistry
Bio.config.DBRegistry.EUtilsDB
Bio.config.DBRegistry.IndexedFileDB
Bio.config.FormatRegistry.FormatGroup
Bio.config.FormatRegistry.FormatObject
Bio.config.FormatRegistry.FormatRegistry
Bio.config.Registry.RegisterableGroup
Bio.config.Registry.RegisterableObject
Bio.config._stanzaformat.Stanza
Bio.config._stanzaformat.StanzaFormat
Bio.config._support.make_cached_expression
Bio.kNN.kNN
Bio.writers.SeqRecord.embl.WriteEmbl
Bio.writers.SeqRecord.fasta.WriteFasta
BioSQL.BioSeqDatabase.Adaptor
BioSQL.DBUtils.Generic_dbutils
BioSQL.Loader.DatabaseLoader
BioSQL.Loader.DatabaseRemover
Martel.Dispatch.Callback
Martel.Dispatch.DispatchHandler
Martel.Dispatch.Dispatcher
Martel.Dispatch.Multicall
Martel.Expression.Alt
Martel.Expression.Any
Martel.Expression.Assert
Martel.Expression.Debug
Martel.Expression.FastFeature
Martel.Expression.Group
Martel.Expression.GroupRef
Martel.Expression.HeaderFooter
Martel.Expression.Literal
Martel.Expression.MaxRepeat
Martel.Expression.ParseRecords
Martel.Expression.PassThrough
Martel.Expression.Str
Martel.Generate.GeneratorState
Martel.Generate.HandleRepeatCount
Martel.IterParser.IterHeaderFooter
Martel.IterParser.IterRecords
Martel.Iterator.EventStream
Martel.Iterator.HeaderFooterEventStream
Martel.Iterator.Iterator
Martel.Iterator.IteratorHeaderFooter
Martel.Iterator.IteratorRecords
Martel.Iterator.RecordEventStream
Martel.Iterator.StoreEvents
Martel.LAX.ElementInfo
Martel.Parser.HeaderFooterParser
Martel.Parser.Parser
Martel.Parser.RecordParser
Martel.RecordReader.CountLines
Martel.RecordReader.EndsWith
Martel.RecordReader.Everything
Martel.RecordReader.Nothing
Martel.RecordReader.RecordReader
Martel.RecordReader.StartsWith
Martel.RecordReader.Until
Martel.convert_re.GroupNames
Martel.msre_parse.Pattern
Martel.msre_parse.Tokenizer
Martel.test.support.CheckGood
Martel.test.support.Dump
Martel.test.test_Parser.CountErrors
Martel.test.test_Parser.CountRecords
Martel.test.test_delimiter.CatchFields
Martel.test.test_optimize.GetErrorPos
exceptions.Exception
exceptions.StandardError
exceptions.TypeError
exceptions.ValueError
markupbase.ParserBase
sgmllib.SGMLParser
xml.sax.handler.ContentHandler
xml.sax.xmlreader.XMLReader
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Bio.Alphabet.Alphabet
Bio.EUtils.POM.AttributeList
Bio.EUtils.POM._AttributeType
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reportlab.graphics.widgetbase.PropHolder
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Bio.Application._Argument
Bio.Application._Option
Bio.EUtils.Datatypes.And
Bio.EUtils.Datatypes.Not
Bio.EUtils.Datatypes.Or
Bio.EUtils.POM.Fragments
Bio.EUtils.POM.Text
Bio.InterPro.Record
Bio.SubsMat.BadMatrix
Martel.Expression.AnyEol
Martel.Expression.AtBeginning
Martel.Expression.AtEnd
Martel.Expression.Dot
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Bio.Application
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Bio.EUtils.Config
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Bio.FSSP.FSSPTools.FSSPAlign
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Bio.Nexus.Nexus
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Bio.pairwise2
_AlignmentConsumer
Bio.Blast.NCBIStandalone
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Martel.Time
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Bio.MarkovModel
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Bio.EUtils.POM
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Bio.EUtils.MultiDict
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Bio.expressions.blast.ncbiblast
_blank_buffer
_BlastConsumer
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Bio.Alphabet.IUPAC
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Bio.Wise
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Bio.SubsMat
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Bio.EUtils.Datatypes
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Bio.MaxEntropy
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Martel.Generate
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Bio.Medline._Scanner
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Bio.Std
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Bio.EUtils.parse
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Bio.config.DBRegistry.TextLikeMixin
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Bio.Graphics.BasicChromosome
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Martel.msre_parse
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Bio.config.DBRegistry
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Bio.MultiProc.copen
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Bio.NMR.NOEtools
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Bio.MarkupEditor
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_construct_node
_construct_pattern
_consume_entry
_consume_header
_Consumer
Bio.Compass
_ContentModelGenerator
_convert_ref
_convert_to
_copy_and_check
_corr
Bio.MEME.Motif
_correct_matrix
_count_emissions
_count_transitions
_crossover
Bio.GA.Crossover.GeneralPoint.TwoCrossover
_data_map
_database
_DatabaseReportConsumer
_datafile
_dbids_to_id_string
Bio.EUtils.ThinClient
_decl_otherchars
_default_parser_callback
_DescriptionConsumer
_determine_position
_diagnose_error
_dict
Bio.EUtils.setup
__filename_key
_digest
_digest_with
_dimensions
_dir_class
Martel.Dispatch
_do_callback
Martel.Parser
_do_dispatch_callback
_draw_distributions
_draw_label
_draw_legend
_draw_scatter_plot
_draw_segment
_draw_subcomponents
_draw_title
_drawTimeResize
reportlab.graphics.shapes._DrawTimeResizeable
_DrawTimeResizeable
reportlab.graphics.shapes
_dump
Bio.Parsers.spark
_eliminate
_empty_str
_empty_unistr
_end_BlastOutput_db
_end_BlastOutput_hits
_end_BlastOutput_program
_end_BlastOutput_query_def
_end_BlastOutput_query_len
_end_BlastOutput_reference
_end_BlastOutput_version
_end_elem
Bio.Medline.nlmmedline_001211_format
Bio.Medline.nlmmedline_010319_format
Bio.Medline.nlmmedline_011101_format
Bio.Medline.nlmmedline_031101_format
_end_element
_end_Hit_accession
_end_Hit_def
_end_Hit_id
_end_Hit_len
_end_Hsp_bit_score
_end_Hsp_evalue
_end_Hsp_gaps
_end_Hsp_hit_frame
_end_Hsp_hit_from
_end_Hsp_hseq
_end_Hsp_identity
_end_Hsp_midline
_end_Hsp_positive
_end_Hsp_qseq
_end_Hsp_query_frame
_end_Hsp_query_from
_end_Hsp_score
_end_Parameters_expect
_end_Parameters_filter
_end_Parameters_gap_extend
_end_Parameters_gap_open
_end_Parameters_matrix
_end_Parameters_sc_match
_end_Parameters_sc_mismatch
_end_Statistics_db_len
_end_Statistics_db_num
_end_Statistics_eff_space
_end_Statistics_entropy
_end_Statistics_hsp_len
_end_Statistics_kappa
_end_Statistics_lambda
_endswith_tagtable_newline
Martel.RecordReader
_endswith_tagtable_rest_of_line
_EOF
_escape
_eval_feature_fn
_evalue
_exp_freq_table_from_obs_freq
_exp_logsum
_extract_pattern_hits
Bio.Prosite
_extract_record
Bio.Prosite.Prodoc
_fails_conditions
Bio.ParserSupport
_fast_dbxref_sp_embl
Bio.StdHandler
_fast_dbxref_sp_general
_fast_dbxref_sp_prosite
_file_exists
Bio.AlignAce.Applications
_find_begin_positions
_find_element
_find_end_positions
_find_entry
Bio.Mindy.FlatDB
_find_global_start
_find_groups
Martel.Expression.ExpressionList
_find_index
_find_local_start
_find_min_max
_find_node
_find_quoted_words
Martel.test.test_Time
_find_range
_find_start
_find_start_entry
Bio.NMR.xpktools
_find_wanted_groupref_names
_fitness_cmp
_fix
_fix_newlines
Martel
_fix_varsplic_sequences
_fixup_defs
Bio.Decode
_fixup_query
_fixup_sp_pattern
_flush_text
Bio.InterPro.InterProParser
Bio.Ndb.NdbParser
_footer_next
_format
_FormParser
Bio.Blast.NCBIWWW
_forward
_forward_recursion
_foward_recursion
_freq_from_count
_full_to_half
_generate
_generate_locs
_get
_get_base_info
_get_base_letters
_get_base_replacements
_get_check_names
_get_class
_get_cols
_get_column_info_content
_get_corba_client
_get_db_module
_get_dbids
_get_file_format
_get_first_words
_get_id
_get_indices
_get_len_expected
_get_letter_freqs
_get_motif_dict
_get_new_organism
_get_next_text
Martel.Iterator
_get_nexus_block
_get_ns
_get_num_motifs
_get_ontology_id
_get_opt_string
_get_ranges
_get_recordset_constructor
Bio.EUtils.DBIdsClient
Bio.EUtils.HistoryClient
_get_retriever
_get_selected_names
Bio.FormatIO
_get_signature_dict
_get_taxon_id
_get_term_id
_get_unique_schema
_get_values
_group
_guess_consensus_alphabet
_handle_sigterm
_header_next
_HeaderConsumer
_HSPConsumer
_iis_solve_delta
_IndexerHandler
Bio.Medline.NLMMedlineXML
_init_zero
_InMemoryIndex
Bio.Index
_InMemoryIndex__version
_InMemoryIndex__version_key
_insert_seqfeature_location
_int_str
Bio.Mindy.BaseDB
_IsIn
Martel.LAX
_kill
_kill_comments_and_break_lines
_length
_list_ini_files
Bio.config.SeqDBRegistry
_list_ini_paths
_ListConsumer
Bio.SwissProt.KeyWList
_load
_load_bioentry_date
_load_bioentry_table
_load_biosequence
_load_comment
_load_database
_load_expression
Bio.config.FormatRegistry
_load_first_existing
_load_module
_load_object
_load_reference
_load_registry_objects
_load_seqfeature
_load_seqfeature_basic
_load_seqfeature_locations
_load_seqfeature_qualifiers
_log_transform
_logadd
_logsum
_logvecadd
_lookup_alias
_lookup_location
_lpad
_lpad_until_equal
_make_ambiguous_ranges
Bio.Data.IUPACData
_make_biofetch_db
_make_biosql_db
_make_callback
_make_fast_lookup
Martel.Expression
_make_flat_db
_make_group_pattern
_make_no_case
_make_pickleable
_make_ranges
_make_score_matrix_fast
_make_score_matrix_generic
_make_unique
_MASTConsumer
Bio.MEME.Parser
_MASTScanner
_matrix
_MEMEConsumer
_MEMEScanner
_merge_methods
_minimize_any_range
_minimize_escape_char
_minimize_escape_range
_mle
_modify_leaves
_motifname
_must_have
_must_have_set
_must_not_have
_my_urlencode
_name
_name_n_vector
_namelist
_needs_stripping
_newname
Bio.MultiProc.Task
_non_empty_str
_non_empty_unistr
_normalize
_normalize_expression
_normalize_params
_num_stat
_numoccurrences
_nv
_open
Bio.WWW.ExPASy
Bio.WWW.NCBI
Bio.WWW.SCOP
_openfu
_Option
_options
_pad
_pad_until_equal
_pair_replacement
_ParametersConsumer
_parse
Bio.Blast.NCBIStandalone._DescriptionConsumer
_Parse
_parse_blast_ref_page
_parse_blast_results_page
_parse_buffer
_parse_chain
_parse_constants
Bio.Ndb
_parse_database
_parse_doctype_attlist
_parse_doctype_element
_parse_doctype_entity
_parse_doctype_notation
_parse_doctype_subset
_parse_elements
_parse_fields
_parse_iteration
_parse_link
_parse_list
_parse_nexus_block
_parse_primary_table_entry
_parse_qblast_ref_page
_parse_query
_parse_secondary_table_entry
_parse_sub
_parse_time
_parse_version
_parses_file
_parses_string
_PickleHandle
_Primer3RecordConsumer
Bio.Emboss.Primer
_Primer3Scanner
_PrimerSearchRecordConsumer
_PrimerSearchScanner
_print_name
_ProcHandle
_PSIBlastConsumer
_pvalue
_query_re
Bio.Blast.NCBIStandalone._HSPConsumer
_quote
_random_norm
_re_align
_re_lengths
_re_names
_re_positive_alignment
_re_profilewidth
_re_scores
_re_search
_re_start
_re_threshold
_read
_read_dicts
_read_primary_table
_read_secondary_table
_readline_and_check_start
PublicationDBIdsRecord
SequenceDBIdsRecord
PublicationHistoryRecord
SequenceHistoryRecord
_record_next
_RecordConsumer
Bio.Enzyme
Bio.Gobase
Bio.Medline
Bio.Rebase
Bio.Sequencing.Ace
Bio.Sequencing.Phd
Bio.SwissProt.SProt
_recover_alignments
_replace_parenthesized_ambigs
_resolve
_retrieve_annotations
BioSQL.BioSeq
_retrieve_dbxref
_retrieve_dbxrefs
_retrieve_features
_retrieve_qualifier_value
_retrieve_reference
_retrieve_seq
_retrieve_taxon
_rms
_run_concurrent
_run_serial
_safe_asarray
_safe_copy_and_check
_safe_float
_safe_int
_safe_log
_SavedDataHandle
_scan_3d
Bio.Prosite._Scanner
_scan_abbreviated_pairwise_alignment
Bio.Blast.NCBIWWW._Scanner
_scan_ac
Bio.SwissProt.SProt._Scanner
_scan_accession
Bio.Prosite.Prodoc._Scanner
_scan_Adeno2
Bio.Rebase._Scanner
_scan_alignment
Bio.Compass._Scanner
_scan_alignment_header
Bio.Blast.NCBIStandalone._Scanner
_scan_alignments
_scan_an
Bio.Enzyme._Scanner
_scan_annotated_matches
Bio.MEME.Parser._MASTScanner
_scan_begin_sequence
Bio.Sequencing.Phd._Scanner
_scan_blastform
_scan_bq_data
Bio.Sequencing.Ace._Scanner
_scan_bracket_tags
_scan_ca
_scan_cc
_scan_cf
_scan_comments
_scan_copyright
_scan_copyrights
_scan_database_info
_scan_database_report
_scan_date_entered
_scan_date_modified
_scan_de
_scan_descriptions
_scan_di
_scan_dna
_scan_do
_scan_dr
_scan_dt
_scan_enzyme_num
_scan_field
Bio.Gobase._Scanner
_scan_fns
_scan_footer
Bio.SwissProt.KeyWList._Scanner
_scan_ft
_scan_gene_record
_scan_gn
_scan_header
Bio.MEME.Parser._MEMEScanner
_scan_hsp
_scan_hsp_alignment
_scan_hsp_header
_scan_id
_scan_keywords
_scan_kw
_scan_Lambda
_scan_lengths
_scan_line
_scan_ma
_scan_masterslave_alignment
_scan_matches
_scan_methylation
_scan_microorganism
_scan_motifs
_scan_name
_scan_names
_scan_nr
_scan_oc
_scan_og
_scan_one_pairwise_alignment
_scan_os
_scan_ox
_scan_pa
_scan_pairwise_alignments
_scan_parameters
_scan_pBR322
_scan_PhiX174
_scan_pr
_scan_profilewidth
_scan_prosite_refs
_scan_protein_record
_scan_prototype
_scan_query_info
_scan_ra
_scan_rc
_scan_record
_scan_reference
_scan_refs
_scan_rl
_scan_rn
_scan_rounds
_scan_rp
_scan_rt
_scan_ru
_scan_rx
_scan_scores
_scan_sequence
_scan_sequence_data
_scan_sequence_record
_scan_source
_scan_sq
_scan_SV40
_scan_temperature
_scan_terminator
_scan_text
_scan_threshold
_Scanner
_schema_from_motif
_score
_secure_name
_select_names
_send_to_blasturl
_SeqLength
Bio.Search
_seqmatrix2strmatrix
_seqname
_sequence
_sequence_name
_SequenceConsumer
_set
_set_colors_and_shapes
_set_current_seq
_set_if_given
_set_kind
_set_up_genetic_algorithm
_set_up_wheel
_settag
_ShelveIndex
_ShelveIndex__version
_ShelveIndex__version_key
_sort_keys
_sort_keys_by_values
_stanzaformat
Bio.config
_start
_START
_start_elem
_start_element
_start_Hit
_start_Hsp
_startswith_tagtable_newline
_startswith_tagtable_rest_of_line
_statelabels
_stateset
_strand
_strip_and_combine
_support
Bio.dbdefs
_tabs
_taxlabels
_taxpartition
_taxset
_test
Bio.Wise.psw
_text_in
_toobj
_tostr
_train_iis
_translate
_tree
_treepartition
_treeset
_try_open_read
_try_open_write
_tuplestr
Bio.EUtils.sourcegen
_unhandled
_unhandled_section
_uniform_norm
_unknown_nexus_block
_unmake_pickleable
_use_tag_format
_utree
_validate_attribute
_verify_attributes
_verify_name
_verify_subtypes
_verify_test
Bio.Prosite.Pattern
_version
_viterbi
_walk
_warn
_wrap_kegg
Bio.KEGG
_write_kegg
_write_primary_table
_write_secondary_table
_write_text
_XMLparser
Bio.Blast.NCBIXML
abi_thumbprint
abs
abs_res_num
Bio.FSSP.fssp_rec.align
Abstract
Bio.GA.Selection
abstract
abstract_author
AbstractCommandline
AbstractConsumer
AbstractDPAlgorithms
Bio.HMM.DynamicProgramming
AbstractLayer
Bio.NeuralNetwork.BackPropagation.Layer
AbstractParser
AbstractPosition
Bio.SeqFeature
AbstractSelection
Bio.GA.Selection.Abstract
AbstractTrainer
Bio.HMM.Trainer
acc
accession
Ace
Bio.Sequencing
ACEFileRecord
ACEParser
acquire
Adaptor
BioSQL.BioSeqDatabase
add
add_after
add_align_list
add_attribute
add_before
add_blank
add_class
add_comment
add_count
add_dbid
add_dbxref
add_dbxref_dbids
add_description
add_doc
add_edge
add_entry
add_examples
add_feature_qualifier
add_features
add_filename
Bio.Mindy.BaseDB.WriteDB
add_first_text_handler
add_function
add_group
add_header
add_hsp
add_hsp_seqs
add_import
add_instance
add_instance_from_values
add_int_handler
add_interaction
add_label
add_location
add_method
add_module
add_node
add_primer_set
add_reaction
add_record
add_ref
Bio.EUtils.POM.IDREFS
add_sequence
add_species
add_stats
add_succ
add_table
add_test
add_test_lines
add_text
add_text_block_handler
add_text_decode_handler
add_text_dict_handler
add_text_handler
add_to_logodds
add_to_pssm
add_url
add_value_handler
addnode
address
addRule
af
affine_penalty
Affy
Bio
AfterPosition
Ais
Algorithm
Align
align
Bio.FSSP.fssp_rec
AlignAce
Bio.AlignAce.AlignAceStandalone
AlignAceCommandline
AlignAceConsumer
Bio.AlignAce.Parser
AlignAceParser
AlignAceScanner
Bio.AlignAce.Scanner
AlignAceStandalone
Bio.AlignAce
AlignInfo
Bio.Align
Alignment
Bio.Align.Generic
Bio.Blast.Record
AlignmentColumn
AlignmentColumnFullException
AlignmentHasDifferentLengthsError
Bio.CAPS
all_ids
all_letters_sum
all_pairs
all_unambiguous
allitems
allkeys
allow_all_transitions
allow_transition
allvalues
Alphabet
Bio.Alphabet
alphabet
alphabet_matches
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet
AlphabetEncoder
Alt
alternate_name
ambiguity
AmbiguousCodonTable
Bio.Data.CodonTable
AmbiguousForwardTable
AmbiguousRepair
Bio.GA.Repair.Stabilizing
amplifier
amplifier_length
amplifier_sequence
And
annotations
Any
AnyBut
AnyEol
apad
Bio.EUtils.DTDs.LinkOut
append
Bio.Wise.psw.Alignment
append_sets
Application
application_name
application_version
ApplicationResult
Applications
Bio.Blast
Bio.Emboss
args
asdict
Bio.listfns
Assert
AssertNot
AtBeginning
AtEnd
attempt_read_and_call
ATTLIST
Bio.EUtils.DTDs.LinkOut.IconUrl
Bio.EUtils.DTDs.LinkOut.ObjectUrl
Bio.EUtils.DTDs.LinkOut.Url
Bio.EUtils.DTDs.LinkOut.apad
Bio.EUtils.DTDs.LinkOut.pad
Bio.EUtils.DTDs.LinkOut.strip
Bio.EUtils.DTDs.LinkOut.subs
Bio.EUtils.DTDs.eLink_020511.Id
Bio.EUtils.DTDs.eSummary_020511.Item
Attribute
Bio.EUtils.DTDs.eLink_020511
AttributeList
attributes
AttributesImpl
xml.sax.xmlreader
augment
author
autocommit
BioSQL.DBUtils.Pgdb_dbutils
BioSQL.DBUtils.Psycopg_dbutils
available_results
back_table
back_transcribe
Bio.Seq
Bio.utils
back_translate
backpropagate
BackPropagation
Bio.NeuralNetwork
backward_algorithm
BadMatrix
BarChartDistribution
Bio.Graphics.Distribution
Base
base_str
BaseDB
Bio.Mindy
BaseDBIdsRecordSet
BaseException
exceptions
BaseFlatDB
BaseHistoryRecordSet
BaseSeqRecordIndexer
Bio.Mindy.SimpleSeqRecord
basestring
BasicChromosome
Bio.Graphics
BasicNetwork
Bio.NeuralNetwork.BackPropagation.Network
BaumWelchTrainer
BeforePosition
begin_contig
begin_sequence
BetweenPosition
bf_search
Bio.Pathway.Rep.MultiGraph
BinaryOp
BioCorbaDB
BioformatDBName
Bio.DBXRef
BioSeq
BioSQL
BioSeqDatabase
BioSQLDB
BisectFile
Blast
blast
Bio.expressions
blast_cutoff
Bio.Blast.NCBIStandalone._ParametersConsumer
blastall
BlastallCommandline
Bio.Blast.Applications
BlastErrorParser
BlastParser
blastpgp
BlastTableEntry
Bio.Blast.ParseBlastTable
BlastTableReader
BlastTableRec
blasturl
Block
blocks
Bol
bootstrap
bq_data
bq_header
branchlength2support
Brief
bs
build_align
build_resnum_list
buildASTNode
builders
BuildSearch
Bio.builders.Search.search
BuildSeqRecord
Bio.builders.SeqRecord.sequence
buildState
buildTree
buildTree_r
byte_concat
Bio.HotRand
calc_affine_penalty
calculate
Bio.LogisticRegression
Bio.NaiveBayes
Bio.kNN
calculate_fitness
call
call_method
call_number
Callback
calltag
capitalize
CAPS
CAPSMap
Capture
Martel.test.test_macros
cartesian
cas_registry_number
Case
catalytic_activity
CatchFields
Martel.test.test_delimiter
category
Bio.EUtils.Datatypes.FieldNotFound
Bio.EUtils.Datatypes.OutputMessage
Bio.EUtils.Datatypes.PhraseIgnored
Bio.EUtils.Datatypes.PhraseNotFound
Bio.EUtils.Datatypes.QuotedPhraseNotFound
CDATA
CelConsumer
Bio.Affy.CelFile
CelFile
Bio.Affy
CelParser
CelRecord
CelScanner
center
CGIDB
Chain
Bio.Crystal
Bio.Nexus.Nodes
chain_id
ChainException
characters
CharBuffer
check_assert
check_assert_not
check_at_beginning
check_dicts
Martel.test.test_attrs
check_element
check_error_pos
Martel.test.test_optimize
CheckAssert
CheckAssertNot
CheckGood
Martel.test.support
checkgroup
CheckGroupRef
CheckLinkSet
chem
child_edges
children
chomp
chompchomp
choose_format
chromat_file
Chromosome
ChromosomeCounts
Bio.Graphics.DisplayRepresentation
ChromosomeSegment
Citation
CitationParser
class_update_date
ClassHolder
classify
clear
close
closegroup
ClustalFormat
Bio.SeqIO.generic
cmp_dicts
co_data
co_header
CodonTable
Bio.Data
cofactor
collapse
collectRules
Cols
ColumnUnit
combine
command_line
Commandline
Comment
comment
comments
commit
common_ancestor
Comparative
ComparativeScatterPlot
Bio.Graphics.Comparative
compare
Martel.test.test_Expression
compare_motifs
CompareAce
Bio.AlignAce.CompareAceStandalone
CompareAceCommandline
CompareAceConsumer
CompareAceParser
CompareAceScanner
CompareAceStandalone
Compass
compile
compile_file
Bio.EUtils.dtd2py
complement
compression
compute_accum_weight
Config
Bio.EUtils
config
consensus
Bio.Nexus.Trees
constant
contains
ContentHandler
xml.sax.handler
CONTENTMODEL
Bio.EUtils.DTDs.LinkOut.Attribute
Bio.EUtils.DTDs.LinkOut.Base
Bio.EUtils.DTDs.LinkOut.Brief
Bio.EUtils.DTDs.LinkOut.Database
Bio.EUtils.DTDs.LinkOut.ExclQuery
Bio.EUtils.DTDs.LinkOut.InclQuery
Bio.EUtils.DTDs.LinkOut.Link
Bio.EUtils.DTDs.LinkOut.LinkId
Bio.EUtils.DTDs.LinkOut.LinkSet
Bio.EUtils.DTDs.LinkOut.Name
Bio.EUtils.DTDs.LinkOut.NameAbbr
Bio.EUtils.DTDs.LinkOut.ObjId
Bio.EUtils.DTDs.LinkOut.ObjectList
Bio.EUtils.DTDs.LinkOut.ObjectSelector
Bio.EUtils.DTDs.LinkOut.Provider
Bio.EUtils.DTDs.LinkOut.ProviderId
Bio.EUtils.DTDs.LinkOut.Query
Bio.EUtils.DTDs.LinkOut.Rule
Bio.EUtils.DTDs.LinkOut.RuleToMany
Bio.EUtils.DTDs.LinkOut.Separator
Bio.EUtils.DTDs.LinkOut.SubObjectSelector
Bio.EUtils.DTDs.LinkOut.SubProvider
Bio.EUtils.DTDs.LinkOut.SubjectType
Bio.EUtils.DTDs.LinkOut.UrlName
Bio.EUtils.DTDs.LinkOut.normalize
Bio.EUtils.DTDs.LinkOut.tolower
Bio.EUtils.DTDs.LinkOut.toupper
Bio.EUtils.DTDs.eInfo_020511.Count
Bio.EUtils.DTDs.eInfo_020511.DbInfo
Bio.EUtils.DTDs.eInfo_020511.DbList
Bio.EUtils.DTDs.eInfo_020511.DbName
Bio.EUtils.DTDs.eInfo_020511.DbTo
Bio.EUtils.DTDs.eInfo_020511.Descriptor
Bio.EUtils.DTDs.eInfo_020511.ERROR
Bio.EUtils.DTDs.eInfo_020511.Field
Bio.EUtils.DTDs.eInfo_020511.FiledList
Bio.EUtils.DTDs.eInfo_020511.Hierarchy
Bio.EUtils.DTDs.eInfo_020511.IsDate
Bio.EUtils.DTDs.eInfo_020511.IsNumerical
Bio.EUtils.DTDs.eInfo_020511.Link
Bio.EUtils.DTDs.eInfo_020511.LinkList
Bio.EUtils.DTDs.eInfo_020511.Menu
Bio.EUtils.DTDs.eInfo_020511.MenuName
Bio.EUtils.DTDs.eInfo_020511.Name
Bio.EUtils.DTDs.eInfo_020511.SingleToken
Bio.EUtils.DTDs.eInfo_020511.TermCount
Bio.EUtils.DTDs.eInfo_020511.eInfoResult
Bio.EUtils.DTDs.eLink_020511.Attribute
Bio.EUtils.DTDs.eLink_020511.DbFrom
Bio.EUtils.DTDs.eLink_020511.DbTo
Bio.EUtils.DTDs.eLink_020511.ERROR
Bio.EUtils.DTDs.eLink_020511.IconUrl
Bio.EUtils.DTDs.eLink_020511.IdCheckList
Bio.EUtils.DTDs.eLink_020511.IdList
Bio.EUtils.DTDs.eLink_020511.IdUrlList
Bio.EUtils.DTDs.eLink_020511.IdUrlSet
Bio.EUtils.DTDs.eLink_020511.Info
Bio.EUtils.DTDs.eLink_020511.Link
Bio.EUtils.DTDs.eLink_020511.LinkName
Bio.EUtils.DTDs.eLink_020511.LinkSet
Bio.EUtils.DTDs.eLink_020511.LinkSetDb
Bio.EUtils.DTDs.eLink_020511.Name
Bio.EUtils.DTDs.eLink_020511.NameAbbr
Bio.EUtils.DTDs.eLink_020511.ObjUrl
Bio.EUtils.DTDs.eLink_020511.Provider
Bio.EUtils.DTDs.eLink_020511.Score
Bio.EUtils.DTDs.eLink_020511.SubjectType
Bio.EUtils.DTDs.eLink_020511.Url
Bio.EUtils.DTDs.eLink_020511.eLinkResult
Bio.EUtils.DTDs.ePost_020511.ERROR
Bio.EUtils.DTDs.ePost_020511.Id
Bio.EUtils.DTDs.ePost_020511.InvalidIdList
Bio.EUtils.DTDs.ePost_020511.QueryKey
Bio.EUtils.DTDs.ePost_020511.WebEnv
Bio.EUtils.DTDs.ePost_020511.ePostResult
Bio.EUtils.DTDs.eSearch_020511.Count
Bio.EUtils.DTDs.eSearch_020511.ERROR
Bio.EUtils.DTDs.eSearch_020511.ErrorList
Bio.EUtils.DTDs.eSearch_020511.Explode
Bio.EUtils.DTDs.eSearch_020511.Field
Bio.EUtils.DTDs.eSearch_020511.FieldNotFound
Bio.EUtils.DTDs.eSearch_020511.From
Bio.EUtils.DTDs.eSearch_020511.Id
Bio.EUtils.DTDs.eSearch_020511.IdList
Bio.EUtils.DTDs.eSearch_020511.OP
Bio.EUtils.DTDs.eSearch_020511.OutputMessage
Bio.EUtils.DTDs.eSearch_020511.PhraseIgnored
Bio.EUtils.DTDs.eSearch_020511.PhraseNotFound
Bio.EUtils.DTDs.eSearch_020511.QueryKey
Bio.EUtils.DTDs.eSearch_020511.QueryTranslation
Bio.EUtils.DTDs.eSearch_020511.QuotedPhraseNotFound
Bio.EUtils.DTDs.eSearch_020511.RetMax
Bio.EUtils.DTDs.eSearch_020511.RetStart
Bio.EUtils.DTDs.eSearch_020511.Term
Bio.EUtils.DTDs.eSearch_020511.TermSet
Bio.EUtils.DTDs.eSearch_020511.To
Bio.EUtils.DTDs.eSearch_020511.Translation
Bio.EUtils.DTDs.eSearch_020511.TranslationSet
Bio.EUtils.DTDs.eSearch_020511.TranslationStack
Bio.EUtils.DTDs.eSearch_020511.WarningList
Bio.EUtils.DTDs.eSearch_020511.WebEnv
Bio.EUtils.DTDs.eSearch_020511.eSearchResult
Bio.EUtils.DTDs.eSummary_020511.DocSum
Bio.EUtils.DTDs.eSummary_020511.ERROR
Bio.EUtils.DTDs.eSummary_020511.Id
Bio.EUtils.DTDs.eSummary_020511.eSummaryResult
ContentModel
contents
Contig
converged
ConversionMutation
Bio.GA.Mutation.Simple
convert
Convert
convert_absolute_support
convert_any
Martel.convert_re
convert_assert
convert_assert_not
convert_at
convert_branch
convert_charref
convert_codepoint
convert_entityref
convert_groupref
convert_in
convert_list
convert_literal
convert_max_repeat
convert_newline
convert_not_literal
convert_re
convert_std_feature
convert_subpattern
convert_summary_Date
convert_summary_Date_string
convert_summary_Integer
convert_summary_Items
convert_summary_List
convert_summary_String
convert_summary_Unknown
ConvertDispatchHandler
ConvertHandler
copen
Bio.MultiProc
copen_fn
copen_sys
copy
count
Count
Bio.EUtils.DTDs.eInfo_020511
Bio.EUtils.DTDs.eSearch_020511
count_monomers
count_records
Martel.test.test_RecordReader2
CountErrors
Martel.test.test_Parser
CountLines
CountRecords
country
crc
crc64
Bio.crc
create
create_berkeleydb
create_flatdb
create_lymphocyte
CreateDict
Bio.PropertyManager
crop_matrix
Crossover
Bio.GA
Crystal
CrystalError
cstatus
ct
ct_data
ct_start
Data
data
data_entered
data_modified
data_table
databank_reference
database
Bio.Blast.NCBIStandalone._DatabaseReportConsumer
Database
database_cross_reference
database_info
Bio.Blast.NCBIStandalone._HeaderConsumer
database_length
database_name
database_num_letters
database_num_sequences
database_reference
DatabaseDict
DatabaseInfo
DatabaseLoader
BioSQL.Loader
DatabaseRemover
DatabaseReport
DataRecord
Datatypes
Date
date
date_field
DateRange
dbdefs
DbFrom
DBGroup
dbid
DBIds
dbids
DBIdsClient
DBIdsLookup
DBIdsRecord
DbInfo
DbList
DbName
DBObject
DBRegistry
DBSeq
DBSeqRecord
DBServer
DbTo
DBUtils
DBXRef
dbxref
dbxref_dbid
dbxref_dbname
dbxref_negate
dbxrefs
Debug
Decode
decode
DecodeParser
DecodeScanner
default
DEFAULT_PSEUDO
define_block
Bio.expressions.genbank
del_attribute
del_parser
DelimitedFields
delimiter
Martel.test.testformats
Martel.test.testformats.delimiter
delnode
demo
reportlab.graphics.widgetbase.Widget
description
Description
description_block
description_header
description_line
Descriptor
destroy
destroy_transition
detach
df_search
dict
Dictionary
Bio.PubMed
dictionary_match
DictLookup
difference
DifferentialCutsite
DifferentialSchemaFitness
Bio.NeuralNetwork.Gene.Schema
Digits
disease
DiskFlatDB
Dispatch
Dispatcher
DispatchHandler
display
DisplayRepresentation
distance
Distribution
DistributionPage
Diversity
DiversitySelection
Bio.GA.Selection.Diversity
DNAAlphabet
do_br
do_crossover
do_input
do_it
do_test
DocSum
Bio.EUtils.DTDs.eSummary_020511
documentation
Dot
download_many
draw
draw_to_file
dropoff_1st_pass
ds
dtd2py
dtd_end
dtd_start
DTDConsumerForSourceGeneration
DTDs
dumb_consensus
dump
Dump
Martel.test.test_swissprot38
dump_saved
Bio.FilteredReader
dumpProperties
dye
DynamicProgramming
Bio.HMM
EConsenseCommandline
Bio.Emboss.Applications
edges
efetch
Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin
Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin
Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin
Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin
efetch_using_dbids
efetch_using_history
effective_database_length
effective_hsp_length
effective_query_length
effective_search_space
effective_search_space_used
eInfo_020511
Bio.EUtils.DTDs
eInfoResult
EInvertedCommandline
elapsed
element
Martel.LAX.LAXAttrs
Martel.LAX.LAXPositions
ElementInfo
ElementNode
elink
eLink_020511
elink_using_dbids
elink_using_history
eLinkResult
embl
Bio.formatdefs
Bio.writers.SeqRecord
embl65
Bio.expressions.embl
EMBLFormat
Emboss
empty
Empty
encode
encode_motif
Encodings
end
Bio.StdHandler.Handle_hsp_seqalign
Bio.StdHandler.Handle_search_header
Bio.StdHandler.Handle_search_info
Bio.StdHandler.Handle_search_table
end_
end_a
Bio.UniGene.UniGeneParser
end_alignment
Bio.Blast.NCBIStandalone._AlignmentConsumer
end_b
end_block
end_contig
end_database_report
end_dbid
Bio.StdHandler.Handle_dbid
end_dbxref
end_dbxref_dbid
end_dbxref_dbname
end_description
Bio.StdHandler.Handle_description
end_description_block
end_descriptions
end_fast_dbxref
end_feature
end_feature_block
end_feature_description
end_feature_location
end_feature_qualifier
end_feature_qualifier_description
end_form
end_h1
end_h2
end_header
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end_hsp
end_hsp_frame
end_hsp_seqalign_homology_seq
end_hsp_seqalign_query_leader
end_hsp_seqalign_query_seq
end_hsp_seqalign_subject_seq
end_hsp_value
end_i
end_li
end_ol
end_parameters
end_record
end_search_header
end_search_table
end_search_table_entry
end_search_table_value
end_sequence
Bio.StdHandler.Handle_sequence
end_sequence_block
end_sub
end_table
end_td
end_tr
end_ul
endDocument
endElement
Martel.test.test_macros.Capture
endElementNS
endPrefixMapping
EndsWith
endswith
ENeighborCommandline
english_abstract
ENTITIES
ENTITY
entity_or_charref
entitydefs
entry_date
entry_month
Enumeration
Enzyme
enzyme_num
EnzymeRecord
Eof
Eol
epost
ePost_020511
ePostResult
Bio.EUtils.DTDs.ePost_020511
EProtDistCommandline
EProtParsCommandline
equal_weight
Error
ERROR
error
Martel.msre_constants
xml.sax.handler.ErrorHandler
ErrorHandler
ErrorList
ErrorProblem
escape
esearch
eSearch_020511
eSearchResult
ESeqBootCommandline
Est2GenomeCommandline
estimate_params
esummary
eSummary_020511
esummary_using_dbids
esummary_using_history
eSummaryResult
ETandemCommandline
euclidean
Bio.distance
euclidean_py
EUtils
EUtilsDB
EUtilsError
EUtilsSearchError
EventGenerator
EventStream
Everything
evolve
Evolver
ExactPosition
ExampleManager
Bio.NeuralNetwork.Training
Exception
ExclQuery
execute
execute_and_fetch_col0
execute_and_fetchall
execute_one
expand_template
expandtabs
ExPASy
Bio.WWW
ExPASyDictionary
Explode
export_fasta
Expression
ExpressionList
expressions
extend
ExtendedIUPACDNA
ExtendedIUPACProtein
extract_key
extract_keywords
extract_urls
ExtractUrls
Bio.NetCatch
EZRetrieve
fast_dbxref
FASTA
Bio.SeqIO
fasta
fasta_mult_align
FastacmdCommandline
FastaFormat
FastaReader
Bio.SeqIO.FASTA
FastaWriter
FastFeature
fatalError
fcmp
Bio.mathfns
feature
Feature
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feature_location_end
feature_location_start
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feature_qualifier
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feature_qualifier_name
feature_table
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feed
Bio.Affy.CelFile.CelScanner
Bio.AlignAce.Scanner.AlignAceScanner
Bio.AlignAce.Scanner.CompareAceScanner
fetch
Bio.EUtils.Mixins.PublicationFetchMixin
fetch_dbid_by_dbname
fetch_seqid_by_accession
fetch_seqid_by_display_id
fetch_seqid_by_identifier
fetch_seqid_by_version
fetch_seqids_by_accession
fff_rec
Field
FieldNotFound
File
FiledList
fileno
fill_chromosome
fill_header
fill_hot_cache
filter
Bio.FSSP.FSSPTools
FilteredReader
find
Bio.triefind
find_ambiguous
find_anychar
Bio.stringfns
find_builder
find_differences
find_elements
find_matches
find_related
find_schemas
find_start
find_states
find_submodules
Bio.config._support
find_terms
find_words
find_writer
finish_endtag
finish_shorttag
finish_starttag
fix
fix_punctuation
FixDocumentBuilder
fixspaces
FlatDB
flatten
Float
float_param
float_stat
flush
format_alignment
FormatConvert
FormatConverter
Bio.Align.FormatConvert
formatdefs
FormatGroup
FormatIO
FormatIOIterator
FormatObject
FormatRegistry
formats
forward_algorithm
forward_gc
forward_length
forward_seq
forward_start
forward_table
forward_tm
found_antigen
foundMatch
Fragments
frame
frameshift
FreqTable
Bio.SubsMat.FreqTable
From
from_dbids
from_motifs
from_parser
from_signatures
fromkeys
FSSP
fssp_rec
Bio.FSSP
FSSPAlign
FSSPAlignDict
FSSPAlignRec
FSSPHeader
FSSPMultAlign
FSSPSumDict
FSSPSumRec
FSSPTools
full_repr
fullpath
Function
function_population
Bio.GA.Organism
FunctionCall
FunctionCallChain
FunctionHolder
FunctionIndexer
FunctionName
FuzznucCommandline
GA
gap_char
gap_consensus
gap_penalties
gap_trigger
gap_x_dropoff
gap_x_dropoff_final
gaponly
Gapped
gapped
GCGFormat
gen_iterator
Martel.test.test_IterParser
genbank
genBlank
genClass
genComment
Gene
gene_name
gene_symbol
General
Bio.GA.Crossover
Bio.GA.Mutation
GeneralPoint
GeneralPointCrossover
Bio.GA.Crossover.GeneralPoint
Generate
generate
generate_alt
generate_any
generate_assert
generate_at_beginning
generate_at_end
generate_debug
generate_dot
generate_eol
generate_group
generate_groupref
generate_literal
generate_max_repeat
generate_named_max_repeat
generate_null_op
generate_parser
generate_pass_through
generate_seq
generate_str
GenerationEvolver
Bio.GA.Evolver
GeneratorState
GeneRecord
Generic
generic
Generic_dbutils
BioSQL.DBUtils
generic_run
GenericASTBuilder
GenericASTMatcher
GenericASTTraversal
GenericASTTraversalPruningException
GenericFormat
GenericParser
GenericScanner
GeneticAlgorithmFinder
genFunc
genImport
genMethod
get
get_alignment_length
get_all
get_all_primary_ids
get_all_seqs
get_all_urls
get_as
get_attribute
get_blank_emissions
get_blank_transitions
get_builder
get_characters
get_children
get_column
get_data
get_dbutils
get_differing
get_document
get_dtd_compiler
get_element
get_entry
get_error
get_escape_length
get_generator
get_header
get_id
get_id_dictionary
get_info
get_init_rms
get_instance_by_name
get_interpro_entry
Bio.WWW.InterPro
get_markov_model
get_merge_text
Martel.optimize
get_mod_file
get_motif_by_name
get_motif_matches
get_motif_matches_for_sequence
get_original_taxon_order
get_parent
get_parser
get_prev
get_PrimarySeq_stream
get_prodoc_entry
get_prosite_entry
get_query_params
get_random
get_residue
get_result
get_rms
get_rotran
get_segment_info
get_Seq_by_acc
get_Seq_by_id
get_seq_by_num
get_Seq_by_primary_id
get_Seq_by_ver
get_Seqs_by_acc
get_sourcefile
get_sprot_raw
get_start_end
get_starttag_text
get_subseq_as_string
get_succ
get_supported_features
get_taxa
get_terminals
get_text
get_top
get_top_percentage
get_transformed
get_urls_by_index
get_urls_by_label
get_urls_by_range
getall
getBounds
getContentHandler
getDTDHandler
getEntityResolver
getErrorHandler
GetErrorPos
getException
getFeature
getLength
getMessage
getName
getNameByQName
getNames
getnode
GetObject
getpos
getProperties
getProperty
getQNameByName
getQNames
gettype
Bio.EUtils.Config.DatabaseDict
getType
getValue
getValueByQName
getwidth
global_alphabet
goahead
Gobase
GrabElements
GrabXPathNodes
Bio.Mindy.XPath
Graph
Bio.Pathway.Rep
Bio.Pathway.Rep.Graph
Graphics
group
Group
group_elem
group_names
GroupNames
GroupRef
groups
guess_gaps
handle_charref
handle_comment
handle_data
Handle_dbid
Handle_dbxref
handle_decl
Handle_description
handle_endtag
handle_entityref
Handle_feature_location
Handle_feature_qualifier
Handle_features
Handle_hsp
Handle_hsp_seqalign
handle_pi
Handle_search_header
Handle_search_info
Handle_search_table
Handle_sequence
handle_starttag
HandleRepeatCount
has_attribute
has_attributes
has_children
has_expr
Bio.dbdefs._support
has_group
has_key
has_no_group
has_str
has_trailing_linefeed
hasAttributes
HashSet
Bio.Pathway.Rep.HashSet
HasStopCodon
Header
HEADER
HeaderFooter
HeaderFooterEventStream
HeaderFooterParser
Hetero
hex_convert
HiddenLayer
HiddenMarkovModel
Bio.HMM.MarkovModel
Hierarchy
HistoryClient
HistoryCookie
HistoryLookup
HistoryRecord
Hit
hit
hit_alignment
hit_coverage
hit_description
hit_length
HMM
hmmpfam
HomologySeq
hot_rand
HotCache
HotRand
HotRandom
HPModel
Bio.Alphabet.Reduced
HSP
hsp
hsp_frame
hsp_seqalign
hsp_seqalign_homology_seq
hsp_seqalign_query_end
hsp_seqalign_query_leader
hsp_seqalign_query_name
hsp_seqalign_query_seq
hsp_seqalign_query_start
hsp_seqalign_subject_end
hsp_seqalign_subject_name
hsp_seqalign_subject_seq
hsp_seqalign_subject_start
hsp_strand
hsp_value
hsps_gapped
hsps_no_gap
hsps_prelim_gapped
hsps_prelim_gapped_attempted
HSPSeq
IconUrl
Id
ID
IdCheck
IdCheckList
identification
identify
identifyFile
identifyString
identities
identity_match
IdList
IDREF
IDREFS
IdUrlList
IdUrlSet
IF
ignorableWhitespace
ignore_characters
Immune
Bio.Ais
import_dict
InclQuery
IndentedText
index
Index
index_file
index_many
IndexedFileDB
indexesof
Info
information_content
inherit_indent
InputLayer
insert
insert_element
insert_gap
insert_raw_text
insert_singleton
insert_text
Instance
int_field
int_param
int_stat
intd
Integer
intensities
Interaction
Bio.Pathway
interactions
InterleaveCrossover
internal_gc
internal_length
internal_seq
internal_start
internal_tm
InterPro
interpro
InterProParser
Bio.InterPro
intersection
InvalidIdList
invert
is_absolute_url
is_blank_line
is_char
is_compatible
is_empty
Bio.SGMLExtractor
is_finished
is_firstchar
is_identical
is_mergeable
is_monophyletic
is_parent_of
isAlive
isalnum
isalpha
IsDate
isdigit
islower
isname
isname_with_attrs
IsNumerical
issn
isspace
issue_part_supplement
istitle
isupper
Item
item
itemindex
items
iterate
Iterate
iterateFile
iterateString
Iterator
IteratorHeaderFooter
IteratorRecords
IterHeaderFooter
Martel.IterParser
iteritems
iterkeys
IterParser
IterRecords
itervalues
IUPAC
IUPACAmbiguousDNA
IUPACAmbiguousRNA
IUPACData
IUPACEncoding
Bio.Encodings
IUPACProtein
IUPACUnambiguousDNA
IUPACUnambiguousRNA
join
join_english
join_fixspaces
journal_subset
journal_title_code
ka_params
ka_params_gap
KEGG
keys
KeyWList
Bio.SwissProt
keyword
kill
kNN
KnownStateTrainer
labels
language
LargeFastaFormat
last_id
BioSQL.DBUtils.Mysql_dbutils
last_revision_date
LAX
LAXAttrs
LAXPositions
Layer
Bio.NeuralNetwork.BackPropagation
lazy_auto_immune_check
lcc
lcc_mult
Bio.lcc
lcc_simp
lcheck
Bio.EUtils.Mixins.LinkMixin
lchomp
length
lengths
letter_sum
letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA
Bio.Alphabet.IUPAC.ExtendedIUPACProtein
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA
Bio.Alphabet.IUPAC.IUPACProtein
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA
Bio.Alphabet.Reduced.HPModel
Bio.Alphabet.Reduced.Murphy10
Bio.Alphabet.Reduced.Murphy15
Bio.Alphabet.Reduced.Murphy4
Bio.Alphabet.Reduced.Murphy8
Bio.Alphabet.Reduced.PC5
Bio.Alphabet.SecondaryStructure
Bio.Alphabet.SingleLetterAlphabet
Bio.Alphabet.ThreeLetterProtein
LineDistribution
Link
link
LinkId
LinkList
LinkMixin
Bio.EUtils.Mixins
LinkName
LinkOut
LinkSet
LinkSetDb
LinksLinkSet
list
list_ambiguous_codons
list_any_ids
list_biodatabase_names
list_bioentry_display_ids
list_bioentry_ids
list_possible_proteins
listfns
ListParser
Literal
ljust
llinks
load
Bio.config._stanzaformat
load_database_sql
load_module
load_seqrecord
Loader
local_test_main
Martel.test.run_tests
LocalParser
Location
Bio.Mindy.Location
log_likelihood
LogDPAlgorithms
logistic_function
LogisticRegression
lookup
lower
lowess
Bio.Statistics
Bio.Statistics.lowess
LowQualityBlastError
lstrip
Lymphocyte
lymphocyte_factory
main
Bio.expressions.blast.wublast
major_revision_date
make_1id
Bio.expressions.fasta
make_2id
make_back_table
make_cached_expression
make_consensus
make_decoder
make_entropy
make_expression
make_iterator
make_log_odds_matrix
make_node
make_parser
make_pattern
make_pssm
make_rate_limited_function
make_relative_entropy
make_timed_function
make_typechecked_decoder
make_writer
makedict
makeFIRST
makeRE
mapped_pattern
mapping
MarkovModel
MarkovModelBuilder
MarkupEditor
MartelAttributeList
MASTParser
MASTRecord
match
match_all
match_r
match_sequence
matches_schema
matchpath
mathfns
matrix
MatrixInfo
MaxEntropy
MaxRepeat
Medline
medline
MEME
MEMEMotif
MEMEParser
MEMERecord
MemoryFlatDB
Menu
MenuName
merge_strings
mesh_heading
mesh_tree_number
message
MethodHolder
methylation
microorganism
MidPoint
Mindy
Mixins
ml_estimator
model_sequences
MostCountSchemaFitness
Motif
Bio.AlignAce.Motif
motif
Bio.MEME
Bio.NeuralNetwork.Gene
motif_hit
motif_mask
motif_name
motif_score
MotifCoder
Bio.NeuralNetwork.Gene.Motif
MotifFinder
mro
msre_constants
msre_parse
mult_align
multalign
Multicall
MulticallEnd
MulticallStart
MultiDict
MultiGraph
MultipleAlignment
MultiProc
Murphy10
Murphy15
Murphy4
Murphy8
must_not_parse
must_parse
MutableSeq
mutate
mutate_and_crossover
Mutation
MyParser
Bio.File
Mysql_dbutils
NaiveBayes
Name
name_filter
NameAbbr
names
NCBI
ncbiblast
Bio.expressions.blast
NCBICodonTable
NCBICodonTableDNA
NCBICodonTableRNA
NCBIStandalone
NCBIWWW
NCBIXML
ncheck
ncols
Ndb
NdbParser
neighbor_links
NeighborLinkSet
NetCatch
Network
NeuralNetwork
new_attribute
new_database
new_element_type
new_external_entity
new_external_pe
new_general_entity
new_group_tag
new_notation
new_parameter_entity
next
next_id
next_nonwhitespace
next_num
next_until
next_word
Nexus
Bio.Nexus
NexusError
NexusFormat
nlmmedline_001211_format
nlmmedline_010319_format
nlmmedline_011101_format
nlmmedline_031101_format
NLMMedlineXML
NMR
NMTOKEN
NMTOKENS
no_author
no_hits
nobuffer
NoCase
node
Node
NodeData
NodeException
Nodes
nodes
NOEtools
Bio.NMR
noevent
nonmodel_sequences
nonterminal
normalize
Not
Nothing
npix
nrows
nucleotide_alphabet
Bio.Data.CodonTable.NCBICodonTableDNA
Bio.Data.CodonTable.NCBICodonTableRNA
NucleotideAlphabet
NullOp
num_Adeno2
num_ambiguous
num_extends
num_good_extends
num_hits
num_Lambda
num_left
num_letters_in_database
num_matches
num_pBR322
num_PhiX174
num_running
num_seqs_better_e
num_sequences
num_sequences_in_database
num_SV40
Number
number_of_references
numerical_results
ObjectList
ObjectParserHandler
ObjectSelector
ObjectUrl
ObjId
ObjUrl
observed_frequency_to_substitution_matrix
OneOfPosition
OP
open
open_database
open_file
Bio.Mindy.compression
OpenDB
opengroup
Opt
optimize
optimize_unnamed_groups
optimize_unnamed_groups_recursive
Or
order
OrderedMultiDict
organelle
Organism
organism_classification
organism_species
original_taxon_order
OutputLayer
OutputMessage
p_arg
p_args
p_expression
p_term
pad
pagination
pairlist_to_dict
pairwise2
PalindromeCommandline
parameter
parameters
Parameters
parent_edges
parents
parse
Bio.ParserSupport.AbstractParser
parse_comment
parse_declaration
parse_endtag
parse_fetch_identifiers
parse_fetch_publication_xml
parse_fetch_sequence_xml
parse_file
parse_lcheck
parse_line
parse_link_xml
parse_llinks
parse_marked_section
parse_neighbor_links
parse_pi
parse_post
parse_search
parse_simple_xpath
parse_single
Bio.EZRetrieve
parse_starttag
parse_str
parse_summary_xml
parse_template
parse_using_dtd
ParseAlignment
ParseBlastTable
parseFile
ParseNexus
Parser
ParserBase
markupbase
ParseRecords
ParserException
ParserIncompleteException
ParserPositionException
ParserRecordException
Parsers
ParserSupport
parseString
partition
PassThrough
pathname
Pathway
Pattern
pattern
pattern_mapping
PatternHit
PatternIO
Bio.NeuralNetwork.Gene.Pattern
PatternRepository
PC5
pdb
pdb_reference
pdb_res_num
Peaklist
peek
peek_nonwhitespace
peek_word
peekline
percent_monomers
personal_name_as_subject
Pgdb_dbutils
Phd
PhraseIgnored
PhraseNotFound
phred_version
pick_a_lymphocyte
PirFormat
pmfetch
pmneighbor
pmqty
Point
poll
POM
POMDocument
pop
popitem
pos_align_list2dict
pos_specific_score_matrix
PosAlign
PositionGap
positive_alignment
post
posted_date
postorder
PostResult
predict
predictNOE
preorder
prepare_input_source
Bio.EUtils.ReseekFile
preprocess
pretty_print_prediction
Bio.HMM.Utilities
primary_key_name
PrimaryNamespace
PrimaryTable
Primer
primer3_format
Primer3Commandline
Primer3Parser
Primer3Primers
Primer3Record
primer_name
primersearch_format
PrimerSearchAmplifier
PrimerSearchCommandline
PrimerSearchInputRecord
PrimerSearchOutputRecord
PrimerSearchParser
print_debug
print_full_mat
print_info
print_info_content
Bio.Align.AlignInfo
print_item
print_mat
print_matrix
prlinks
Problem
processing_instruction
processingInstruction
Prodoc
prodoc
product_size
profilewidth
PropertyManager
PropHolder
reportlab.graphics.widgetbase
Prosite
prosite
prosite_reference
prosite_to_grouped_re
prosite_to_re
PrositeAlphabet
PrositeMatch
PrositeTerm
protein_alphabet
ProteinAlphabet
ProteinRecord
prototype
provideNode
reportlab.graphics.shapes.UserNode
Provider
ProviderId
prune
PSIBlast
PSIBlastParser
PSSM
psw
Psycopg_dbutils
publication_date
publication_type
PublicationDBIdsFetchMixin
PublicationDBIdsRecordSet
PublicationFetchMixin
PublicationHistoryFetchMixin
PublicationHistoryRecordSet
PubMed
pubmed_id
Punctuation
pwm
qa
qblast
quality_levels
query
Query
query_alignment
query_coverage
query_description
query_description_block
query_info
query_length
query_size
QueryKey
QueryTranslation
QuotedPhraseNotFound
quotestrip
random_motif
random_population
random_test
randomize
RandomMotifGenerator
Range
rd
rd_data
rd_header
Re
Reaction
reactions
read
read_and_call
read_and_call_until
read_and_call_while
read_block
read_config
read_count
read_dna
read_freq
read_fssp
read_repr
read_text_matrix
read_to_end
ReaderError
readFile
ReadIntensity
readline
readlines
Reads
ReadSeq
readString
Rebase
recalculate_fitness
RecognizeHandler
Record
record
Bio.UniGene
record_originator
RecordEventStream
RecordParser
RecordReader
reduce_sequence
Reduced
reference
Reference
reference_author
reference_comment
reference_cross_reference
reference_location
reference_number
reference_position
reference_title
reflect
register
register_ncbi_table
RegisterableGroup
Bio.config.Registry
RegisterableObject
Registry
remainder
RemapEnd
RemapStart
remove
remove_database
remove_edge
remove_empty_line
remove_leading_whitespace
remove_node
remove_polyA
remove_reaction
remove_succ
remove_useless_dot
Rep
Rep1
Repair
repair
reparent
replace
replace_entry
replace_groups
replace_text
replacement_dictionary
RepN
report_unbalanced
representation
RequestLimiter
res_name
ReseekFile
reset
residue_dict
resolve
resolve_class
rest
RetMax
retrieve_single
RetStart
reverse
reverse_complement
reverse_gc
reverse_length
reverse_name
reverse_seq
reverse_start
reverse_tm
rfind
rfind_anychar
rindex
rint
rjust
RNAAlphabet
rollback
root_with_outgroup
RouletteWheel
RouletteWheelSelection
Bio.GA.Selection.RouletteWheel
round
Round
Rows
rpartition
rpsblast
rsplit
rstrip
rt
rt_data
rt_start
Rule
rule
RuleToMany
run
run_tests
Martel.test
safe_exp
safe_int
safe_load_module
safe_log
safe_log2
safe_peekline
safe_readline
SafeFitnessCrossover
Bio.GA.Crossover.General
SafeFitnessMutation
Bio.GA.Mutation.General
safename
save
save_characters
save_info
saveline
SAXException
xml.sax._exceptions
sbjct
scale_segment_value
ScaledDPAlgorithms
scan
scan_sequence_expasy
Scanner
scanprosite1
Scheduler
Bio.MultiProc.Scheduler
Schema
SchemaCoder
SchemaDNAAlphabet
SchemaFactory
SchemaFinder
SCOP
score
Score
score_hit
scores
scramble
search
Search
Bio.builders
Bio.builders.Search
search_accum_weight
search_for
search_header
search_instances
search_parameter
search_pwm
search_statistic
search_table
search_table_description
search_table_entry
search_table_value
search_taxon
SearchResult
secondary_key_names
secondary_source_id
SecondaryNamespace
SecondaryStructure
SecondaryTable
seek
select
select_at_random
select_names
Selection
Separator
Seq
seq
SeqDBRegistry
SeqFeature
SeqIO
SeqMat
SeqRecord
Bio.SeqRecord
Bio.writers
sequence
Bio.builders.SeqRecord
sequence_block
sequence_data
sequence_header
SequenceDBIdsFetchMixin
SequenceDBIdsRecordSet
SequenceFetchMixin
SequenceHistoryFetchMixin
SequenceHistoryRecordSet
SequenceParser
SequenceRecord
sequences
Sequencing
set
set_attribute
set_data
set_defaults
set_dirty
set_emission_pseudocount
set_emission_score
set_equal_probabilities
set_id
set_indented
set_inline
set_level
set_mask
set_namespace
set_original_taxon_order
set_parameter
set_prev
set_random_probabilities
set_scale
set_subtree
set_succ
set_text
set_transition_pseudocount
set_transition_score
set_weight
setCharacterSaver
setContentHandler
setdefault
setDocumentLocator
setDTDHandler
setEntityResolver
setErrorHandler
setFeature
SetGroupValue
setliteral
setLocale
setLocation
Martel.Parser.ParserException
setName
setnode
setnomoretags
setProperties
setProperty
setup
severity
Bio.EUtils.Datatypes.ErrorProblem
Bio.EUtils.Datatypes.WarningProblem
SGMLExtractor
SGMLExtractorHandle
SGMLHandle
SGMLParser
sgmllib
SGMLStripper
SGMLStrippingConsumer
ShortQueryBlastError
Signature
SignatureCoder
Bio.NeuralNetwork.Gene.Signature
SignatureFinder
sim
Simple
Martel.test.testformats.swissprot38
simple_elem
SimpleFinisher
SimpleIndexer
SimpleRecordFilter
SimpleSeqRecord
simplify
single_primer_line
SingleLetterAlphabet
SinglePointCrossover
Bio.GA.Crossover.Point
SinglePositionMutation
SingleToken
sink
sink_interactions
size
skip_empty_group
skip_whitespace
SkipLinesTo
SkipLinesUntil
skippedEntity
smprint
sort
source
source_interactions
SourceFile
sourcegen
SourceGen
Spaces
span
spark
Bio.Parsers
special_list
species
split
splitany
splitlines
SProt
sprot_search_de
sprot_search_ful
SS
Bio.expressions.transfac
ss1
Stabilizing
Bio.GA.Repair
StandardError
Stanza
StanzaFormat
start
start_
start_a
start_aa_list
start_alignment
start_alphabet
start_b
start_block
start_codons
start_database_report
start_dbid
start_dbxref
start_dbxref_dbid
start_dbxref_dbname
start_dbxref_negate
start_description
start_description_block
start_descriptions
start_fast_dbxref
start_feature
start_feature_block
start_feature_description
start_feature_location
start_feature_qualifier
start_feature_qualifier_description
start_form
start_h1
start_h2
start_header
start_hit
start_hsp
start_hsp_frame
start_hsp_seqalign
start_hsp_seqalign_homology_seq
start_hsp_seqalign_query_leader
start_hsp_seqalign_query_seq
start_hsp_seqalign_subject_seq
start_hsp_strand
start_hsp_value
start_i
start_keywords
start_li
start_ol
start_parameters
start_primer
start_record
start_search_table
start_search_table_entry
start_search_table_value
start_sequence
start_sequence_block
start_sub
start_table
start_td
start_tr
start_ul
startDocument
Martel.test.test_attrs.GrabElements
startElement
startElementNS
StartIntensity
startPrefixMapping
starts_with
StartsWith
startswith
Statistics
Std
stdevs
StdHandler
SteadyStateEvolver
StepMatrix
stochiometry
stop_codons
stop_symbol
stopping_criteria
StopTraining
Storage
StoreEvents
Str
str
Str1
strand
String
stringfns
strip
subcomponent_size
subheadings
SubjectType
SubObjectSelector
SubPattern
SubProvider
subs
SubsMat
substance_name
sum
sum_2ple
sum_branchlength
summary
Bio.EUtils.DBIdsClient.DBIdsRecord
Summary
SummaryInfo
superdir
support
SVDSuperimposer
Bio.SVDSuperimposer
Bio.SVDSuperimposer.SVDSuperimposer
swapcase
SwissProt
swissprot
swissprot38
System
t_close_paren
t_comma
t_default
t_float
t_functionname
t_open_paren
t_pipe
t_string
t_whitespace
TableInfo
TaggingConsumer
take
take_byfn
Task
taxonomy_id
tell
TelomereSegment
temperature
Term
TermCount
terminal
terminal_gap_to_missing
terminator
TermSet
test
Martel.test.test_Generate
Martel.test.test_Iterator
Martel.test.test_LAX
Martel.test.test_ParseRecords
Martel.test.test_RecordReader
Martel.test.test_convert_re
test1
test10
test11
test12
test13
test14
test15
test16
test17
test18
test19
test2
test20
test3
test4
test5
test6
test7
test8
test9
test__add__
test__or__
test_alt
test_any
test_assert
test_at_beginning
test_at_end
test_attrs
test_convert_re
test_count
test_count_lines
test_count_lines_lines
test_DelimitedFields
test_delimiter
test_Digits
test_docstring
test_dot
test_end
test_end_lines
test_endswith
test_endswith_errors
test_endswith_exhaustive
test_endswith_generic
test_endswith_remainder
test_endswith_SP
test_escape
test_everything
test_everything_lines
test_expand
test_Expression
test_fasta
test_file
test_filter
test_Float
test_Generate
test_group
test_group_names
test_groupref
test_header_footer1
test_header_footer2
test_header_footer3
test_header_footer4
test_header_footer5
test_header_footer6
test_header_footer7
test_header_footer8
test_header_footer_parser
test_hf1
test_hf2
test_hf3
test_hf4
test_hf5
test_hf6
test_hf7
test_hf8
test_Iterator
test_IterParser
test_LAX
test_literal
test_macros
test_make_iterparsers1
test_make_iterparsers2
test_max_repeat
test_minimize
test_missing_end1
test_missing_end2
test_missing_end3
test_multi
test_nocase
test_nodes
test_none
test_nothing
test_nothing_lines
test_null_op
test_optimize
test_Parser
test_ParseRecords
test_Punctuation
test_reader_parser
test_reads
test_record_parser
test_RecordReader
test_RecordReader2
test_ri1
test_ri2
test_ri3
test_same_tag
test_seq
test_single
test_Spaces
test_start
test_start_lines
test_startswith
test_startswith_errors
test_startswith_exhaustive
test_startswith_generic
test_startswith_remainder
test_startswith_SP
test_str
test_string
test_swissprot38
test_syntax
test_terms
test_Time
test_times
test_ToEol
test_ToSep
test_Unprintable
test_until
test_until_lines
test_valid_names
test_Word
testformats
text
Text
text_field
TextLikeMixin
ThinClient
ThreeLetterProtein
threshold
time
Time
time_file
timetuple
title
title_abbreviation
tname
To
to_clustal
to_fasta
to_file
to_generic
to_string
ToEol
Token
tokenize
Tokenizer
tolower
tomutable
ToSep
toseq
tostring
total_weight
total_weight_range
toupper
Tournament
TournamentSelection
Bio.GA.Selection.Tournament
tr
trace
trace_array_max_index
trace_array_min_index
trace_peak_area_ratio
track_position
train
train_bw
train_visible
Trainer
Training
TrainingExample
TrainingSequence
TranalignCommandline
transcribe
Transcribe
Bio.Transcribe
transfac
transformation
transitions_from
translate
Translate
translate_to_stop
Translation
TranslationError
TranslationSet
TranslationStack
Translator
Bio.Translate
transliterated_title
Tree
TreeError
Trees
triefind
trim
tune
turn3
turn4
turn5
two_mat_DJS
two_mat_relative_entropy
TwoCrossover
TwoPoint
TwoPointCrossover
Bio.GA.Crossover.TwoPoint
TypeError
typestring
undefined
UndoHandle
unescape
unescape_C
unescape_entities
ungap
unhandled
unhandled_section
Uniform
UniformCrossover
Bio.GA.Crossover.Uniform
UniGene
UniGeneParser
union
unique_identifier
unknown-3079434052
unknown_charref
unknown_decl
unknown_endtag
unknown_entityref
unknown_starttag
UnknownDBName
unlink
UnorderedMultiDict
Unprintable
unroot
Until
UntilEol
UntilSep
update
update_emissions
update_transitions
updatepos
upper
Url
UrlName
use_lowercase
use_truecase
use_uppercase
UsePOMParser
UserNode
uses_tags
Utilities
utils
VALID_FORMATS
validate
validate_element
validate_key
ValidationError
ValidationIncreaseStop
Bio.NeuralNetwork.StopTraining
ValueError
values
ValueToken
verify
verify_alphabet
verify_pattern
version
viterbi
volume_issue
wa
wa_data
wa_start
wait
WARNING
warning
WarningList
WarningProblem
WaterCommandline
WebEnv
weighted_stepmatrix
weighting
Widget
window_size
Wise
WithinNDays
WithinPosition
Word
word_field
wr
wr_data
wr_start
wrap_line
write
write_config
write_header
write_nexus_data
write_nexus_data_partitions
write_paths
write_record
write_records
write_repr
write_seq
write_xmlfile
WriteDB
WriteEmbl
Bio.writers.SeqRecord.embl
WriteEmpty
Bio.writers.SeqRecord.empty
WriteFasta
Bio.writers.SeqRecord.fasta
writefile
writefileobject
writeFooter
writeHeader
writeln
Writer
Bio.Writer
writers
wublast
WWW
XMLAttribute
XMLReader
XPath
xpath_index
XpkEntry
xpktools
year
zfill