biopython
v1.71.0
- Bio.Affy.CelFile
- Bio.Affy.CelFile.ParserError
- Bio.Affy.CelFile.Record
- Bio.Align.AlignInfo
- Bio.Align.AlignInfo.PSSM
- Bio.Align.AlignInfo.SummaryInfo
- Bio.AlignIO.ClustalIO
- Bio.AlignIO.ClustalIO.ClustalIterator
- Bio.AlignIO.ClustalIO.ClustalWriter
- Bio.AlignIO.EmbossIO
- Bio.AlignIO.EmbossIO.EmbossIterator
- Bio.AlignIO.EmbossIO.EmbossWriter
- Bio.AlignIO.FastaIO
- Bio.AlignIO.Interfaces
- Bio.AlignIO.Interfaces.AlignmentIterator
- Bio.AlignIO.Interfaces.AlignmentWriter
- Bio.AlignIO.Interfaces.SequentialAlignmentWriter
- Bio.AlignIO.MafIO
- Bio.AlignIO.MafIO.MafIndex
- Bio.AlignIO.MafIO.MafWriter
- Bio.AlignIO.MauveIO
- Bio.AlignIO.MauveIO.MauveIterator
- Bio.AlignIO.MauveIO.MauveWriter
- Bio.AlignIO.NexusIO
- Bio.AlignIO.NexusIO.NexusWriter
- Bio.AlignIO.PhylipIO
- Bio.AlignIO.PhylipIO.PhylipIterator
- Bio.AlignIO.PhylipIO.RelaxedPhylipIterator
- Bio.AlignIO.PhylipIO.RelaxedPhylipWriter
- Bio.AlignIO.PhylipIO.SequentialPhylipIterator
- Bio.AlignIO.PhylipIO.SequentialPhylipWriter
- Bio.AlignIO.StockholmIO
- Bio.AlignIO.StockholmIO.StockholmIterator
- Bio.AlignIO.StockholmIO.StockholmWriter
- Bio.Alphabet.IUPAC
- 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
- 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.Blast.Applications
- Bio.Blast.Applications.NcbiblastformatterCommandline
- Bio.Blast.NCBIStandalone
- Bio.Blast.NCBIStandalone.BlastErrorParser
- Bio.Blast.NCBIStandalone.BlastParser
- Bio.Blast.NCBIStandalone.Iterator
- Bio.Blast.NCBIStandalone.LowQualityBlastError
- Bio.Blast.NCBIStandalone.PSIBlastParser
- Bio.Blast.NCBIStandalone.ShortQueryBlastError
- Bio.Blast.NCBIWWW
- Bio.Blast.NCBIXML
-
Bio.Blast.NCBIXML.BlastParser
- Top
- Summary
-
Functions
- __init__/0
- _end_BlastOutput_db/0
- _end_BlastOutput_hits/0
- _end_BlastOutput_program/0
- _end_BlastOutput_query_ID/0
- _end_BlastOutput_query_def/0
- _end_BlastOutput_query_len/0
- _end_BlastOutput_reference/0
- _end_BlastOutput_version/0
- _end_Hit_accession/0
- _end_Hit_def/0
- _end_Hit_id/0
- _end_Hsp_align_len/0
- _end_Hsp_bit_score/0
- _end_Hsp_evalue/0
- _end_Hsp_gaps/0
- _end_Hsp_hit_frame/0
- _end_Hsp_hit_from/0
- _end_Hsp_hit_to/0
- _end_Hsp_hseq/0
- _end_Hsp_identity/0
- _end_Hsp_midline/0
- _end_Hsp_positive/0
- _end_Hsp_qseq/0
- _end_Hsp_query_frame/0
- _end_Hsp_query_from/0
- _end_Hsp_query_to/0
- _end_Hsp_score/0
- _end_Iteration_query_ID/0
- _end_Iteration_query_def/0
- _end_Iteration_query_len/0
- _end_Parameters_expect/0
- _end_Parameters_filter/0
- _end_Parameters_gap_extend/0
- _end_Parameters_gap_open/0
- _end_Parameters_matrix/0
- _end_Parameters_sc_match/0
- _end_Parameters_sc_mismatch/0
- _end_Statistics_db_len/0
- _end_Statistics_db_num/0
- _end_Statistics_eff_space/0
- _end_Statistics_entropy/0
- _end_Statistics_hsp_len/0
- _end_Statistics_kappa/0
- _end_Statistics_lambda/0
- reset/0
- Bio.Blast.ParseBlastTable
- Bio.Blast.ParseBlastTable.BlastTableEntry
- Bio.Blast.ParseBlastTable.BlastTableReader
- Bio.Blast.ParseBlastTable.BlastTableRec
- Bio.Blast.Record
- 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.Data.CodonTable
- Bio.Data.CodonTable.AmbiguousCodonTable
- Bio.Data.CodonTable.AmbiguousForwardTable
- Bio.Data.CodonTable.CodonTable
- Bio.Data.CodonTable.NCBICodonTable
- Bio.Data.CodonTable.NCBICodonTableDNA
- Bio.Data.CodonTable.NCBICodonTableRNA
- Bio.Data.CodonTable.TranslationError
- Bio.Data.IUPACData
- Bio.Data.SCOPData
- Bio.DocSQL
- Bio.DocSQL.Create
- Bio.DocSQL.Insert
- Bio.DocSQL.IterationCursor
- Bio.DocSQL.NoInsertionError
- Bio.DocSQL.Query
- Bio.DocSQL.QueryAll
- Bio.DocSQL.QueryAllFirstItem
- Bio.DocSQL.QueryGeneric
- Bio.DocSQL.QueryRow
- Bio.DocSQL.QuerySingle
- Bio.DocSQL.Update
- Bio.Emboss.Applications
- Bio.Emboss.Applications.DiffseqCommandline
- Bio.Emboss.Applications.EInvertedCommandline
- Bio.Emboss.Applications.ETandemCommandline
- Bio.Emboss.Applications.Est2GenomeCommandline
- Bio.Emboss.Applications.FConsenseCommandline
- Bio.Emboss.Applications.FDNADistCommandline
- Bio.Emboss.Applications.FDNAParsCommandline
- Bio.Emboss.Applications.FNeighborCommandline
- Bio.Emboss.Applications.FProtDistCommandline
- Bio.Emboss.Applications.FProtParsCommandline
- Bio.Emboss.Applications.FSeqBootCommandline
- Bio.Emboss.Applications.FTreeDistCommandline
- Bio.Emboss.Applications.FuzznucCommandline
- Bio.Emboss.Applications.NeedleCommandline
- Bio.Emboss.Applications.NeedleallCommandline
- Bio.Emboss.Applications.PalindromeCommandline
- Bio.Emboss.Applications.PrimerSearchCommandline
- Bio.Emboss.Applications.SeqmatchallCommandline
- Bio.Emboss.Applications.SeqretCommandline
- Bio.Emboss.Applications.StretcherCommandline
- Bio.Emboss.Applications.TranalignCommandline
- Bio.Emboss.Applications.WaterCommandline
- Bio.Emboss.Primer3
- Bio.Emboss.Primer3.Primers
- Bio.Emboss.Primer3.Record
- Bio.Emboss.PrimerSearch
- Bio.Emboss.PrimerSearch.Amplifier
- Bio.Emboss.PrimerSearch.InputRecord
- Bio.Emboss.PrimerSearch.OutputRecord
- Bio.Entrez.Parser
- Bio.Entrez.Parser.CorruptedXMLError
- Bio.Entrez.Parser.DataHandler
- Bio.Entrez.Parser.DictionaryElement
- Bio.Entrez.Parser.IntegerElement
- Bio.Entrez.Parser.ListElement
- Bio.Entrez.Parser.NotXMLError
- Bio.Entrez.Parser.StringElement
- Bio.Entrez.Parser.StructureElement
- Bio.Entrez.Parser.UnicodeElement
- Bio.Entrez.Parser.ValidationError
- Bio.ExPASy.Enzyme
- Bio.ExPASy.Enzyme.Record
- Bio.ExPASy.Prodoc
- Bio.ExPASy.Prodoc.Record
- Bio.ExPASy.Prodoc.Reference
- Bio.ExPASy.Prosite
- Bio.ExPASy.Prosite.Record
- Bio.ExPASy.ScanProsite
- Bio.ExPASy.ScanProsite.ContentHandler
- Bio.ExPASy.ScanProsite.Parser
- Bio.ExPASy.ScanProsite.Record
- Bio.FSSP.FSSPTools
- Bio.FSSP.FSSPTools.FSSPAlign
- Bio.FSSP.FSSPTools.FSSPMultAlign
- Bio.File.UndoHandle
- Bio.GA.Crossover.General
- Bio.GA.Crossover.General.SafeFitnessCrossover
- Bio.GA.Crossover.GeneralPoint
- Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
- Bio.GA.Crossover.GeneralPoint.InterleaveCrossover
- Bio.GA.Crossover.GeneralPoint.TwoCrossover
- Bio.GA.Crossover.Point
- Bio.GA.Crossover.Point.SinglePointCrossover
- Bio.GA.Crossover.TwoPoint
- Bio.GA.Crossover.TwoPoint.TwoPointCrossover
- Bio.GA.Crossover.Uniform
- Bio.GA.Crossover.Uniform.UniformCrossover
- Bio.GA.Evolver
- Bio.GA.Evolver.GenerationEvolver
- Bio.GA.Evolver.SteadyStateEvolver
- Bio.GA.Mutation.General
- Bio.GA.Mutation.General.SafeFitnessMutation
- Bio.GA.Mutation.Simple
- Bio.GA.Mutation.Simple.ConversionMutation
- Bio.GA.Mutation.Simple.SinglePositionMutation
- Bio.GA.Organism
- Bio.GA.Organism.Organism
- Bio.GA.Repair.Stabilizing
- Bio.GA.Repair.Stabilizing.AmbiguousRepair
- Bio.GA.Selection.Abstract
- Bio.GA.Selection.Abstract.AbstractSelection
- Bio.GA.Selection.Diversity
- Bio.GA.Selection.Diversity.DiversitySelection
- Bio.GA.Selection.RouletteWheel
- Bio.GA.Selection.RouletteWheel.RouletteWheelSelection
- Bio.GA.Selection.Tournament
- Bio.GA.Selection.Tournament.TournamentSelection
- Bio.GenBank.Record
- Bio.GenBank.Record.Feature
- Bio.GenBank.Record.Qualifier
- Bio.GenBank.Record.Record
- Bio.GenBank.Record.Reference
- Bio.GenBank.Scanner
- Bio.GenBank.Scanner.EmblScanner
- Bio.Geo.Record
- Bio.Geo.Record.Record
- Bio.Graphics.BasicChromosome
- Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment
- Bio.Graphics.BasicChromosome.Chromosome
- Bio.Graphics.BasicChromosome.ChromosomeSegment
- Bio.Graphics.BasicChromosome.Organism
- Bio.Graphics.BasicChromosome.SpacerSegment
- Bio.Graphics.BasicChromosome.TelomereSegment
- Bio.Graphics.ColorSpiral
- Bio.Graphics.ColorSpiral.ColorSpiral
- Bio.Graphics.Comparative
- Bio.Graphics.Comparative.ComparativeScatterPlot
- Bio.Graphics.DisplayRepresentation
- Bio.Graphics.DisplayRepresentation.ChromosomeCounts
- Bio.Graphics.Distribution
- Bio.Graphics.Distribution.BarChartDistribution
- Bio.Graphics.Distribution.DistributionPage
- Bio.Graphics.Distribution.LineDistribution
- Bio.Graphics.KGML_vis
- Bio.Graphics.KGML_vis.KGMLCanvas
- Bio.HMM.DynamicProgramming
- Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
- Bio.HMM.DynamicProgramming.LogDPAlgorithms
- Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
- Bio.HMM.MarkovModel
- Bio.HMM.MarkovModel.HiddenMarkovModel
-
Bio.HMM.MarkovModel.MarkovModelBuilder
- Top
- Summary
-
Functions
- __init__/0
- _all_blank/0
- _all_pseudo/0
- allow_all_transitions/0
- allow_transition/0
- destroy_transition/0
- get_markov_model/0
- set_emission_pseudocount/0
- set_emission_score/0
- set_equal_probabilities/0
- set_initial_probabilities/0
- set_random_emission_probabilities/0
- set_random_initial_probabilities/0
- set_random_probabilities/0
- set_random_transition_probabilities/0
- set_transition_pseudocount/0
- set_transition_score/0
- Bio.HMM.Trainer
- Bio.HMM.Trainer.AbstractTrainer
- Bio.HMM.Trainer.BaumWelchTrainer
- Bio.HMM.Trainer.KnownStateTrainer
- Bio.HMM.Trainer.TrainingSequence
- Bio.HMM.Utilities
- Bio.Index
- Bio.KDTree.KDTree
- Bio.KDTree.KDTree.KDTree
- Bio.KEGG.KGML.KGML_parser
- Bio.KEGG.KGML.KGML_parser.KGMLParser
- Bio.KEGG.KGML.KGML_pathway
- Bio.KEGG.KGML.KGML_pathway.Component
- Bio.KEGG.KGML.KGML_pathway.Entry
- Bio.KEGG.KGML.KGML_pathway.Graphics
- Bio.KEGG.KGML.KGML_pathway.Pathway
- Bio.KEGG.KGML.KGML_pathway.Reaction
- Bio.KEGG.KGML.KGML_pathway.Relation
- Bio.KEGG.REST
- Bio.LogisticRegression
- Bio.LogisticRegression.LogisticRegression
- Bio.MarkovModel
- Bio.MarkovModel.MarkovModel
- Bio.NMR.NOEtools
- Bio.NaiveBayes
- Bio.NaiveBayes.NaiveBayes
- Bio.NeuralNetwork.BackPropagation.Layer
- Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer
- Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer
- Bio.NeuralNetwork.BackPropagation.Layer.InputLayer
- Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
- Bio.NeuralNetwork.BackPropagation.Network
- Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
- Bio.NeuralNetwork.Gene.Motif
- Bio.NeuralNetwork.Gene.Motif.MotifCoder
- Bio.NeuralNetwork.Gene.Motif.MotifFinder
- Bio.NeuralNetwork.Gene.Pattern
- Bio.NeuralNetwork.Gene.Pattern.PatternIO
- Bio.NeuralNetwork.Gene.Pattern.PatternRepository
- Bio.NeuralNetwork.Gene.Schema
- 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.SchemaDNAAlphabet
- Bio.NeuralNetwork.Gene.Schema.SchemaFactory
- Bio.NeuralNetwork.Gene.Schema.SchemaFinder
- Bio.NeuralNetwork.Gene.Schema.SimpleFinisher
- Bio.NeuralNetwork.Gene.Signature
- Bio.NeuralNetwork.Gene.Signature.SignatureCoder
- Bio.NeuralNetwork.Gene.Signature.SignatureFinder
- Bio.NeuralNetwork.StopTraining
- Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop
- Bio.NeuralNetwork.Training
- Bio.NeuralNetwork.Training.ExampleManager
- Bio.NeuralNetwork.Training.TrainingExample
- Bio.Nexus.Nexus
- Bio.Nexus.Nexus.Block
- Bio.Nexus.Nexus.CharBuffer
- Bio.Nexus.Nexus.Commandline
-
Bio.Nexus.Nexus.Nexus
- Top
- Summary
-
Functions
- __init__/0
- _adjust/0
- _adjust_charlabels/0
- _apply_block_structure/0
- _charlabels/0
- _charpartition/0
- _charset/0
- _check_taxlabels/0
- _codonposset/0
- _get_indices/0
- _get_nexus_block/0
- _matrix/0
- _name_n_vector/0
- _parse_list/0
- _parse_nexus_block/0
- _resolve/0
- _taxlabels/0
- _taxpartition/0
- _taxset/0
- _translate/0
- _utree/0
- add_sequence/0
- append_sets/0
- bootstrap/0
- constant/0
- crop_matrix/0
- cstatus/0
- export_fasta/0
- export_phylip/0
- gaponly/0
- get_original_taxon_order/0
- insert_gap/0
- invert/0
- read/0
- set_original_taxon_order/0
- terminal_gap_to_missing/0
- weighted_stepmatrix/0
- write_nexus_data/0
- write_nexus_data_partitions/0
- Bio.Nexus.Nexus.NexusError
- Bio.Nexus.Nexus.StepMatrix
- Bio.Nexus.Nodes
- Bio.Nexus.Nodes.Chain
- Bio.Nexus.Nodes.ChainException
- Bio.Nexus.Nodes.Node
- Bio.Nexus.Nodes.NodeException
- Bio.Nexus.StandardData
- Bio.Nexus.StandardData.NexusError
- Bio.Nexus.StandardData.StandardData
- Bio.Nexus.Trees
- Bio.Nexus.Trees.NodeData
-
Bio.Nexus.Trees.Tree
- Top
- Summary
-
Functions
- __init__/0
- __str__/0
- _add_nodedata/0
- _add_subtree/0
- _connect_subtree/0
- _get_values/0
- _parse/0
- _walk/0
- branchlength2support/0
- collapse_genera/0
- common_ancestor/0
- convert_absolute_support/0
- count_terminals/0
- display/0
- distance/0
- get_taxa/0
- get_terminals/0
- has_support/0
- is_bifurcating/0
- is_compatible/0
- is_identical/0
- is_internal/0
- is_monophyletic/0
- is_preterminal/0
- is_terminal/0
- ladderize_nodes/0
- make_info_string/0
- merge_with_support/0
- newickize/0
- node/0
- prune/0
- randomize/0
- search_taxon/0
- set_subtree/0
- split/0
- sum_branchlength/0
- to_string/0
- unroot/0
- Bio.Nexus.Trees.TreeError
- Bio.PDB.AbstractPropertyMap
- Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap
- Bio.PDB.AbstractPropertyMap.AbstractPropertyMap
- Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap
- Bio.PDB.Atom
-
Bio.PDB.Atom.Atom
- Top
- Summary
-
Functions
- __init__/0
- __repr__/0
- __sub__/0
- _assign_element/0
- copy/0
- detach_parent/0
- flag_disorder/0
- get_altloc/0
- get_anisou/0
- get_bfactor/0
- get_coord/0
- get_full_id/0
- get_fullname/0
- get_id/0
- get_name/0
- get_occupancy/0
- get_parent/0
- get_sigatm/0
- get_siguij/0
- get_vector/0
- is_disordered/0
- set_anisou/0
- set_parent/0
- set_sigatm/0
- set_siguij/0
- transform/0
- Bio.PDB.Atom.DisorderedAtom
- Bio.PDB.Chain
- Bio.PDB.Chain.Chain
- Bio.PDB.DSSP.DSSP
- Bio.PDB.Dice
- Bio.PDB.Dice.ChainSelector
- Bio.PDB.Entity
- Bio.PDB.Entity.DisorderedEntityWrapper
- Bio.PDB.Entity.Entity
- Bio.PDB.FragmentMapper
- Bio.PDB.FragmentMapper.Fragment
- Bio.PDB.FragmentMapper.FragmentMapper
- Bio.PDB.HSExposure
- Bio.PDB.HSExposure.ExposureCN
- Bio.PDB.HSExposure.HSExposureCA
- Bio.PDB.HSExposure.HSExposureCB
- Bio.PDB.MMCIF2Dict
- Bio.PDB.MMCIF2Dict.MMCIF2Dict
- Bio.PDB.MMCIFParser
- Bio.PDB.MMCIFParser.FastMMCIFParser
- Bio.PDB.MMCIFParser.MMCIFParser
- Bio.PDB.Model
- Bio.PDB.Model.Model
- Bio.PDB.NACCESS
- Bio.PDB.NACCESS.NACCESS
- Bio.PDB.NeighborSearch
- Bio.PDB.NeighborSearch.NeighborSearch
- Bio.PDB.PDBExceptions
- Bio.PDB.PDBExceptions.PDBConstructionException
- Bio.PDB.PDBExceptions.PDBConstructionWarning
- Bio.PDB.PDBExceptions.PDBException
- Bio.PDB.PDBIO
- Bio.PDB.PDBIO.PDBIO
- Bio.PDB.PDBIO.Select
- Bio.PDB.PDBList
- Bio.PDB.PDBParser
- Bio.PDB.PDBParser.PDBParser
- Bio.PDB.PSEA
- Bio.PDB.PSEA.PSEA
- Bio.PDB.Polypeptide
- Bio.PDB.Polypeptide.CaPPBuilder
- Bio.PDB.Polypeptide.PPBuilder
- Bio.PDB.Polypeptide.Polypeptide
- Bio.PDB.Residue
- Bio.PDB.Residue.DisorderedResidue
- Bio.PDB.Residue.Residue
- Bio.PDB.ResidueDepth
- Bio.PDB.ResidueDepth.ResidueDepth
- Bio.PDB.Selection
- Bio.PDB.Structure
- Bio.PDB.Structure.Structure
- Bio.PDB.StructureAlignment
- Bio.PDB.StructureAlignment.StructureAlignment
- Bio.PDB.StructureBuilder
- Bio.PDB.StructureBuilder.StructureBuilder
- Bio.PDB.Superimposer
- Bio.PDB.Superimposer.Superimposer
- Bio.PDB.Vector
- Bio.PDB.Vector.Vector
- Bio.ParserSupport
- Bio.ParserSupport.AbstractConsumer
- Bio.ParserSupport.AbstractParser
- Bio.ParserSupport.TaggingConsumer
- Bio.Pathway.Rep.Graph
- Bio.Pathway.Rep.Graph.Graph
- Bio.Pathway.Rep.MultiGraph
- Bio.Pathway.Rep.MultiGraph.MultiGraph
- Bio.Phylo.BaseTree
- Bio.Phylo.BaseTree.BranchColor
- Bio.Phylo.BaseTree.Clade
- Bio.Phylo.BaseTree.Tree
- Bio.Phylo.BaseTree.TreeElement
-
Bio.Phylo.BaseTree.TreeMixin
- Top
- Summary
-
Functions
- _filter_search/0
- collapse/0
- collapse_all/0
- common_ancestor/0
- count_terminals/0
- depths/0
- distance/0
- find_any/0
- find_clades/0
- find_elements/0
- get_nonterminals/0
- get_path/0
- get_terminals/0
- is_bifurcating/0
- is_monophyletic/0
- is_parent_of/0
- is_preterminal/0
- ladderize/0
- prune/0
- split/0
- total_branch_length/0
- trace/0
- Bio.Phylo.CDAO
- Bio.Phylo.CDAO.Clade
- Bio.Phylo.CDAO.Tree
- Bio.Phylo.CDAOIO
- Bio.Phylo.CDAOIO.CDAOError
- Bio.Phylo.CDAOIO.Parser
- Bio.Phylo.CDAOIO.Writer
- Bio.Phylo.Consensus
- Bio.Phylo.NeXML
- Bio.Phylo.NeXML.Clade
- Bio.Phylo.NeXML.Tree
- Bio.Phylo.NeXMLIO
- Bio.Phylo.NeXMLIO.NeXMLError
- Bio.Phylo.NeXMLIO.Parser
- Bio.Phylo.NeXMLIO.Writer
- Bio.Phylo.Newick
- Bio.Phylo.Newick.Clade
- Bio.Phylo.Newick.Tree
- Bio.Phylo.NewickIO
- Bio.Phylo.NewickIO.NewickError
- Bio.Phylo.NewickIO.Parser
- Bio.Phylo.NewickIO.Writer
- Bio.Phylo.PhyloXML
- Bio.Phylo.PhyloXML.Accession
- Bio.Phylo.PhyloXML.Annotation
- Bio.Phylo.PhyloXML.BinaryCharacters
- Bio.Phylo.PhyloXML.BranchColor
- Bio.Phylo.PhyloXML.Clade
- Bio.Phylo.PhyloXML.CladeRelation
- Bio.Phylo.PhyloXML.Confidence
- Bio.Phylo.PhyloXML.Date
- Bio.Phylo.PhyloXML.Distribution
- Bio.Phylo.PhyloXML.DomainArchitecture
- Bio.Phylo.PhyloXML.Events
- Bio.Phylo.PhyloXML.Id
- Bio.Phylo.PhyloXML.MolSeq
- Bio.Phylo.PhyloXML.Other
- Bio.Phylo.PhyloXML.PhyloElement
- Bio.Phylo.PhyloXML.PhyloXMLWarning
- Bio.Phylo.PhyloXML.Phylogeny
- Bio.Phylo.PhyloXML.Phyloxml
- Bio.Phylo.PhyloXML.Point
- Bio.Phylo.PhyloXML.Polygon
- Bio.Phylo.PhyloXML.Property
- Bio.Phylo.PhyloXML.ProteinDomain
- Bio.Phylo.PhyloXML.Reference
- Bio.Phylo.PhyloXML.Sequence
- Bio.Phylo.PhyloXML.SequenceRelation
- Bio.Phylo.PhyloXML.Taxonomy
- Bio.Phylo.PhyloXMLIO
- Bio.Phylo.PhyloXMLIO.Parser
- Bio.Phylo.PhyloXMLIO.PhyloXMLError
- Bio.Phylo.PhyloXMLIO.Writer
- Bio.Phylo.TreeConstruction
- Bio.Phylo.TreeConstruction.DistanceCalculator
- Bio.Phylo.TreeConstruction.DistanceMatrix
- Bio.Phylo.TreeConstruction.DistanceTreeConstructor
- Bio.Phylo.TreeConstruction.NNITreeSearcher
- Bio.Phylo.TreeConstruction.ParsimonyScorer
- Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor
- Bio.Phylo.TreeConstruction.Scorer
- Bio.Phylo.TreeConstruction.TreeConstructor
- Bio.Phylo.TreeConstruction.TreeSearcher
- Bio.PopGen.GenePop.Controller
- Bio.PopGen.GenePop.Controller.GenePopController
- Bio.PopGen.GenePop.EasyController
- Bio.PopGen.GenePop.EasyController.EasyController
- Bio.PopGen.GenePop.FileParser
- Bio.PopGen.GenePop.FileParser.FileRecord
- Bio.PopGen.GenePop.LargeFileParser
- Bio.PopGen.GenePop.LargeFileParser.Record
- Bio.PopGen.GenePop.Utils
- Bio.Restriction.PrintFormat.PrintFormat
- Bio.Restriction.RanaConfig
- Bio.Restriction.Restriction
- Bio.Restriction.Restriction.AbstractCut
- Bio.Restriction.Restriction.Ambiguous
-
Bio.Restriction.Restriction.Analysis
- Top
- Summary
-
Functions
- __init__/0
- _boundaries/0
- _sub_set/0
- _test_normal/0
- _test_reverse/0
- between/0
- blunt/0
- change/0
- defined/0
- do_not_cut/0
- format_output/0
- full/0
- only_between/0
- only_outside/0
- outside/0
- overhang3/0
- overhang5/0
- print_that/0
- show_only_between/0
- with_N_sites/0
- with_name/0
- with_number_list/0
- with_site_size/0
- with_sites/0
- without_site/0
- Bio.Restriction.Restriction.Blunt
- Bio.Restriction.Restriction.Commercially_available
- Bio.Restriction.Restriction.Defined
- Bio.Restriction.Restriction.FormattedSeq
- Bio.Restriction.Restriction.Meth_Dep
- Bio.Restriction.Restriction.Meth_Undep
- Bio.Restriction.Restriction.NoCut
- Bio.Restriction.Restriction.NonPalindromic
- Bio.Restriction.Restriction.NotDefined
- Bio.Restriction.Restriction.Not_available
- Bio.Restriction.Restriction.OneCut
- Bio.Restriction.Restriction.Ov3
- Bio.Restriction.Restriction.Ov5
- Bio.Restriction.Restriction.Palindromic
- Bio.Restriction.Restriction.RestrictionBatch
- Bio.Restriction.Restriction.RestrictionType
- Bio.Restriction.Restriction.TwoCuts
- Bio.Restriction.Restriction.Unknown
- Bio.Restriction.Restriction_Dictionary
- Bio.SCOP.Cla
- Bio.SCOP.Cla.Index
- Bio.SCOP.Cla.Record
- Bio.SCOP.Des
- Bio.SCOP.Des.Record
- Bio.SCOP.Dom
- Bio.SCOP.Dom.Record
- Bio.SCOP.Hie
- Bio.SCOP.Hie.Record
- Bio.SCOP.Raf
- Bio.SCOP.Raf.Res
- Bio.SCOP.Raf.SeqMap
- Bio.SCOP.Raf.SeqMapIndex
- Bio.SCOP.Residues
- Bio.SCOP.Residues.Residues
- Bio.SearchIO.BlatIO
- Bio.SearchIO.BlatIO.BlatPslIndexer
- Bio.SearchIO.BlatIO.BlatPslParser
- Bio.SearchIO.BlatIO.BlatPslWriter
- Bio.SearchIO.FastaIO.FastaM10Indexer
- Bio.SearchIO.FastaIO.FastaM10Parser
- Bio.Seq
- Bio.Seq.MutableSeq
-
Bio.Seq.Seq
- Top
- Summary
-
Functions
- __add__/0
- __contains__/0
- __eq__/0
- __getitem__/0
- __hash__/0
- __init__/0
- __le__/0
- __len__/0
- __lt__/0
- __ne__/0
- __radd__/0
- __repr__/0
- __str__/0
- _get_seq_str_and_check_alphabet/0
- back_transcribe/0
- complement/0
- count/0
- count_overlap/0
- endswith/0
- find/0
- lower/0
- lstrip/0
- reverse_complement/0
- rfind/0
- rsplit/0
- rstrip/0
- split/0
- startswith/0
- strip/0
- tomutable/0
- tostring/0
- transcribe/0
- translate/0
- ungap/0
- upper/0
- Bio.Seq.UnknownSeq
- Bio.SeqFeature
- Bio.SeqFeature.AbstractPosition
- Bio.SeqFeature.AfterPosition
- Bio.SeqFeature.BeforePosition
- Bio.SeqFeature.BetweenPosition
- Bio.SeqFeature.ExactPosition
- Bio.SeqFeature.FeatureLocation
- Bio.SeqFeature.OneOfPosition
- Bio.SeqFeature.PositionGap
- Bio.SeqFeature.Reference
- Bio.SeqFeature.UncertainPosition
- Bio.SeqFeature.UnknownPosition
- Bio.SeqFeature.WithinPosition
- Bio.SeqIO.AbiIO
- Bio.SeqIO.AceIO
- Bio.SeqIO.FastaIO
- Bio.SeqIO.FastaIO.FastaWriter
- Bio.SeqIO.IgIO
- Bio.SeqIO.InsdcIO
- Bio.SeqIO.InsdcIO.EmblWriter
- Bio.SeqIO.InsdcIO.GenBankWriter
- Bio.SeqIO.InsdcIO.ImgtWriter
- Bio.SeqIO.Interfaces
- Bio.SeqIO.Interfaces.SequenceIterator
- Bio.SeqIO.Interfaces.SequenceWriter
- Bio.SeqIO.Interfaces.SequentialSequenceWriter
- Bio.SeqIO.PdbIO
- Bio.SeqIO.PhdIO
- Bio.SeqIO.PhdIO.PhdWriter
- Bio.SeqIO.PirIO
- Bio.SeqIO.PirIO.PirWriter
- Bio.SeqIO.QualityIO.FastqPhredWriter
- Bio.SeqIO.QualityIO.QualPhredWriter
- Bio.SeqIO.SeqXmlIO
- Bio.SeqIO.SeqXmlIO.SeqXmlIterator
- Bio.SeqIO.SeqXmlIO.SeqXmlWriter
- Bio.SeqIO.SeqXmlIO.XMLRecordIterator
- Bio.SeqIO.SffIO
- Bio.SeqIO.SffIO.SffWriter
- Bio.SeqIO.SwissIO
- Bio.SeqIO.TabIO
- Bio.SeqIO.TabIO.TabWriter
- Bio.SeqIO.UniprotIO
- Bio.SeqIO.UniprotIO.Parser
- Bio.SeqRecord
- Bio.SeqUtils.CheckSum
- Bio.SeqUtils.CodonUsage
- Bio.SeqUtils.CodonUsage.CodonAdaptationIndex
- Bio.SeqUtils.CodonUsageIndices
- Bio.SeqUtils.IsoelectricPoint
- Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint
- Bio.SeqUtils.MeltingTemp
- Bio.SeqUtils.ProtParam
- Bio.SeqUtils.ProtParam.ProteinAnalysis
- Bio.SeqUtils.ProtParamData
- Bio.Sequencing.Ace.ACEFileRecord
- Bio.Sequencing.Ace.Reads
- Bio.Sequencing.Phd
- Bio.Sequencing.Phd.Record
- Bio.SubsMat.FreqTable
- Bio.SubsMat.FreqTable.FreqTable
- Bio.SubsMat.MatrixInfo
- Bio.SwissProt.KeyWList
- Bio.SwissProt.KeyWList.Record
- Bio.UniProt.GOA
- Biopython