API Contents:
Bio package
BioSQL package
Biopython
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Index
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Index
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__abs__() (Bio.Phylo.PhyloXML.Confidence method)
__abstractmethods__ (Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer attribute)
(Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute)
(Bio.SearchIO.BlatIO.BlatPslIndexer attribute)
(Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer attribute)
(Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser attribute)
(Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer attribute)
(Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser attribute)
(Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer attribute)
(Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser attribute)
(Bio.SearchIO.FastaIO.FastaM10Indexer attribute)
(Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer attribute)
(Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer attribute)
(Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer attribute)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer attribute)
(Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer attribute)
(Bio.SeqIO.AbiIO.AbiIterator attribute)
(Bio.SeqIO.FastaIO.FastaIterator attribute)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute)
(Bio.SeqIO.GckIO.GckIterator attribute)
(Bio.SeqIO.IgIO.IgIterator attribute)
(Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator attribute)
(Bio.SeqIO.InsdcIO.EmblIterator attribute)
(Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator attribute)
(Bio.SeqIO.InsdcIO.GenBankIterator attribute)
(Bio.SeqIO.InsdcIO.ImgtIterator attribute)
(Bio.SeqIO.Interfaces.SequenceIterator attribute)
(Bio.SeqIO.NibIO.NibIterator attribute)
(Bio.SeqIO.PdbIO.PdbSeqresIterator attribute)
(Bio.SeqIO.PirIO.PirIterator attribute)
(Bio.SeqIO.QualityIO.FastqPhredIterator attribute)
(Bio.SeqIO.QualityIO.QualPhredIterator attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute)
(Bio.SeqIO.SffIO.SffIterator attribute)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute)
(Bio.SeqIO.TabIO.TabIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaIterator attribute)
__add__() (Bio.Align.MultipleSeqAlignment method)
(Bio.codonalign.codonalignment.CodonAlignment method)
(Bio.Crystal.Chain method)
(Bio.PDB.vectors.Vector method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.SCOP.Raf.SeqMap method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqRecord.SeqRecord method)
(Bio.SubsMat.SeqMat method)
(BioSQL.BioSeq.DBSeq method)
__annotations__ (Bio.PDB.internal_coords.IC_Residue attribute)
__array_finalize__() (Bio.Align.substitution_matrices.Array method)
__array_prepare__() (Bio.Align.substitution_matrices.Array method)
__array_ufunc__() (Bio.Align.substitution_matrices.Array method)
__array_wrap__() (Bio.Align.substitution_matrices.Array method)
__bool__() (Bio.Phylo.BaseTree.Clade method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqRecord.SeqRecord method)
__call__() (Bio.Application.AbstractCommandline method)
(Bio.pairwise2.affine_penalty method)
(Bio.pairwise2.dictionary_match method)
(Bio.pairwise2.identity_match method)
__contains__() (Bio.Align.substitution_matrices.Array method)
(Bio.Crystal.Chain method)
(Bio.Crystal.Crystal method)
(Bio.Data.CodonTable.AmbiguousForwardTable method)
(Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.FragmentMapper.FragmentMapper method)
(Bio.PDB.vectors.Vector method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.Phylo.PhyloXML.Events method)
(Bio.Seq.Seq method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqRecord.SeqRecord method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
__delitem__() (Bio.Crystal.Chain method)
(Bio.Crystal.Crystal method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.Entity method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.Phylo.PhyloXML.Events method)
(Bio.Seq.MutableSeq method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
__divmod__() (Bio.Phylo.PhyloXML.Confidence method)
__enter__() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
__eq__() (Bio.Align.PairwiseAlignment method)
(Bio.Crystal.Chain method)
(Bio.Crystal.Hetero method)
(Bio.Entrez.Parser.NoneElement method)
(Bio.motifs.jaspar.Motif method)
(Bio.Pathway.Reaction method)
(Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.Edron method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqFeature.Reference method)
(Bio.SeqRecord.SeqRecord method)
__exit__() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
__float__() (Bio.Phylo.PhyloXML.Confidence method)
__floordiv__() (Bio.Phylo.PhyloXML.Confidence method)
__format__() (Bio.Align.MultipleSeqAlignment method)
(Bio.Align.PairwiseAlignment method)
(Bio.Align.substitution_matrices.Array method)
(Bio.motifs.Motif method)
(Bio.Phylo.BaseTree.Tree method)
(Bio.SeqRecord.SeqRecord method)
__ge__() (Bio.Align.PairwiseAlignment method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.Edron method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.SeqRecord.SeqRecord method)
__getattr__() (Bio.Data.CodonTable.AmbiguousCodonTable method)
(Bio.Graphics.GenomeDiagram.Feature method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
__getitem__() (Bio.Align.AlignInfo.PSSM method)
(Bio.Align.MultipleSeqAlignment method)
(Bio.Align.PairwiseAlignments method)
(Bio.Align.substitution_matrices.Array method)
(Bio.codonalign.codonalignment.CodonAlignment method)
(Bio.Crystal.Chain method)
(Bio.Crystal.Crystal method)
(Bio.Data.CodonTable.AmbiguousForwardTable method)
(Bio.FSSP.fssp_rec.fff_rec method)
(Bio.Graphics.GenomeDiagram.Diagram method)
(Bio.Graphics.GenomeDiagram.FeatureSet method)
(Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.Graphics.GenomeDiagram.GraphSet method)
(Bio.Graphics.GenomeDiagram.Track method)
(Bio.motifs.mast.Record method)
(Bio.motifs.matrix.GenericPositionMatrix method)
(Bio.motifs.meme.Record method)
(Bio.motifs.minimal.Record method)
(Bio.Nexus.StandardData.StandardData method)
(Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.FragmentMapper.FragmentMapper method)
(Bio.PDB.vectors.Vector method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.BaseTree.Clade method)
(Bio.Phylo.PhyloXML.Events method)
(Bio.Phylo.PhyloXML.Phyloxml method)
(Bio.SCOP.Cla.Index method)
(Bio.SCOP.Raf.SeqMap method)
(Bio.SCOP.Raf.SeqMapIndex method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqRecord.SeqRecord method)
(BioSQL.BioSeq.DBSeq method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
__getnewargs__() (Bio.PDB.internal_coords.AtomKey.fieldsDef method)
(Bio.SeqFeature.BetweenPosition method)
(Bio.SeqFeature.OneOfPosition method)
(Bio.SeqFeature.WithinPosition method)
__gt__() (Bio.Align.PairwiseAlignment method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.Edron method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.SeqRecord.SeqRecord method)
__hash__ (Bio.Align.PairwiseAlignment attribute)
(Bio.Crystal.Chain attribute)
(Bio.Crystal.Hetero attribute)
(Bio.Entrez.Parser.NoneElement attribute)
(Bio.Pathway.Rep.Graph.Graph attribute)
(Bio.Pathway.Rep.MultiGraph.MultiGraph attribute)
(Bio.phenotype.phen_micro.PlateRecord attribute)
(Bio.phenotype.phen_micro.WellRecord attribute)
(Bio.Seq.MutableSeq attribute)
(Bio.SeqFeature.CompoundLocation attribute)
(Bio.SeqFeature.FeatureLocation attribute)
(Bio.SeqFeature.Reference attribute)
(Bio.SeqRecord.SeqRecord attribute)
__hash__() (Bio.motifs.jaspar.Motif method)
(Bio.Pathway.Interaction method)
(Bio.Pathway.Reaction method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.Edron method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.Seq method)
(Bio.SeqFeature.UnknownPosition method)
__iadd__() (Bio.Crystal.Chain method)
(Bio.SCOP.Raf.SeqMap method)
__imul__() (Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(BioSQL.BioSeq.DBSeq method)
__init__() (Bio.Affy.CelFile.ParserError method)
(Bio.Affy.CelFile.Record method)
(Bio.Align.AlignInfo.PSSM method)
(Bio.Align.AlignInfo.SummaryInfo method)
(Bio.Align.Applications.ClustalOmegaCommandline method)
(Bio.Align.Applications.ClustalwCommandline method)
(Bio.Align.Applications.DialignCommandline method)
(Bio.Align.Applications.MafftCommandline method)
(Bio.Align.Applications.MSAProbsCommandline method)
(Bio.Align.Applications.MuscleCommandline method)
(Bio.Align.Applications.PrankCommandline method)
(Bio.Align.Applications.ProbconsCommandline method)
(Bio.Align.Applications.TCoffeeCommandline method)
(Bio.Align.MultipleSeqAlignment method)
(Bio.Align.PairwiseAligner method)
(Bio.Align.PairwiseAlignment method)
(Bio.Align.PairwiseAlignments method)
(Bio.AlignIO.Interfaces.AlignmentIterator method)
(Bio.AlignIO.Interfaces.AlignmentWriter method)
(Bio.AlignIO.Interfaces.SequentialAlignmentWriter method)
(Bio.AlignIO.MafIO.MafIndex method)
(Bio.AlignIO.MauveIO.MauveWriter method)
(Bio.Application.AbstractCommandline method)
(Bio.Application.ApplicationError method)
(Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
(Bio.Blast.Applications.NcbiblastformatterCommandline method)
(Bio.Blast.Applications.NcbiblastnCommandline method)
(Bio.Blast.Applications.NcbiblastpCommandline method)
(Bio.Blast.Applications.NcbiblastxCommandline method)
(Bio.Blast.Applications.NcbideltablastCommandline method)
(Bio.Blast.Applications.NcbimakeblastdbCommandline method)
(Bio.Blast.Applications.NcbipsiblastCommandline method)
(Bio.Blast.Applications.NcbirpsblastCommandline method)
(Bio.Blast.Applications.NcbirpstblastnCommandline method)
(Bio.Blast.Applications.NcbitblastnCommandline method)
(Bio.Blast.Applications.NcbitblastxCommandline method)
(Bio.Blast.NCBIXML.BlastParser method)
(Bio.Blast.ParseBlastTable.BlastTableEntry method)
(Bio.Blast.ParseBlastTable.BlastTableReader method)
(Bio.Blast.ParseBlastTable.BlastTableRec method)
(Bio.Blast.Record.Alignment method)
(Bio.Blast.Record.Blast method)
(Bio.Blast.Record.DatabaseReport method)
(Bio.Blast.Record.Description method)
(Bio.Blast.Record.DescriptionExt method)
(Bio.Blast.Record.DescriptionExtItem method)
(Bio.Blast.Record.Header method)
(Bio.Blast.Record.HSP method)
(Bio.Blast.Record.MultipleAlignment method)
(Bio.Blast.Record.Parameters method)
(Bio.Blast.Record.PSIBlast method)
(Bio.Blast.Record.Round method)
(Bio.CAPS.CAPSMap method)
(Bio.CAPS.DifferentialCutsite method)
(Bio.Cluster.Record method)
(Bio.codonalign.codonalignment.CodonAlignment method)
(Bio.codonalign.codonseq.CodonSeq method)
(Bio.Compass.Record method)
(Bio.Crystal.Chain method)
(Bio.Crystal.Crystal method)
(Bio.Crystal.Hetero method)
(Bio.Data.CodonTable.AmbiguousCodonTable method)
(Bio.Data.CodonTable.AmbiguousForwardTable method)
(Bio.Data.CodonTable.CodonTable method)
(Bio.Data.CodonTable.NCBICodonTable method)
(Bio.Emboss.Applications.DiffseqCommandline method)
(Bio.Emboss.Applications.EInvertedCommandline method)
(Bio.Emboss.Applications.Est2GenomeCommandline method)
(Bio.Emboss.Applications.ETandemCommandline method)
(Bio.Emboss.Applications.FConsenseCommandline method)
(Bio.Emboss.Applications.FDNADistCommandline method)
(Bio.Emboss.Applications.FDNAParsCommandline method)
(Bio.Emboss.Applications.FNeighborCommandline method)
(Bio.Emboss.Applications.FProtDistCommandline method)
(Bio.Emboss.Applications.FProtParsCommandline method)
(Bio.Emboss.Applications.FSeqBootCommandline method)
(Bio.Emboss.Applications.FTreeDistCommandline method)
(Bio.Emboss.Applications.FuzznucCommandline method)
(Bio.Emboss.Applications.FuzzproCommandline method)
(Bio.Emboss.Applications.IepCommandline method)
(Bio.Emboss.Applications.NeedleallCommandline method)
(Bio.Emboss.Applications.NeedleCommandline method)
(Bio.Emboss.Applications.PalindromeCommandline method)
(Bio.Emboss.Applications.Primer3Commandline method)
(Bio.Emboss.Applications.PrimerSearchCommandline method)
(Bio.Emboss.Applications.SeqmatchallCommandline method)
(Bio.Emboss.Applications.SeqretCommandline method)
(Bio.Emboss.Applications.StretcherCommandline method)
(Bio.Emboss.Applications.TranalignCommandline method)
(Bio.Emboss.Applications.WaterCommandline method)
(Bio.Emboss.Primer3.Primers method)
(Bio.Emboss.Primer3.Record method)
(Bio.Emboss.PrimerSearch.Amplifier method)
(Bio.Emboss.PrimerSearch.InputRecord method)
(Bio.Emboss.PrimerSearch.OutputRecord method)
(Bio.Entrez.Parser.CorruptedXMLError method)
(Bio.Entrez.Parser.DataHandler method)
(Bio.Entrez.Parser.DictionaryElement method)
(Bio.Entrez.Parser.ListElement method)
(Bio.Entrez.Parser.NoneElement method)
(Bio.Entrez.Parser.NotXMLError method)
(Bio.Entrez.Parser.ValidationError method)
(Bio.ExPASy.cellosaurus.Record method)
(Bio.ExPASy.Enzyme.Record method)
(Bio.ExPASy.Prodoc.Record method)
(Bio.ExPASy.Prodoc.Reference method)
(Bio.ExPASy.Prosite.Record method)
(Bio.ExPASy.ScanProsite.ContentHandler method)
(Bio.ExPASy.ScanProsite.Parser method)
(Bio.ExPASy.ScanProsite.Record method)
(Bio.File.UndoHandle method)
(Bio.FSSP.fssp_rec.fff_rec method)
(Bio.FSSP.FSSPAlignDict method)
(Bio.FSSP.FSSPAlignRec method)
(Bio.FSSP.FSSPHeader method)
(Bio.FSSP.FSSPSumRec method)
(Bio.FSSP.FSSPTools.FSSPMultAlign method)
(Bio.FSSP.PosAlign method)
(Bio.GenBank.FeatureParser method)
(Bio.GenBank.Iterator method)
(Bio.GenBank.Record.Feature method)
(Bio.GenBank.Record.Qualifier method)
(Bio.GenBank.Record.Record method)
(Bio.GenBank.Record.Reference method)
(Bio.GenBank.RecordParser method)
(Bio.GenBank.Scanner.InsdcScanner method)
(Bio.GenBank.utils.FeatureValueCleaner method)
(Bio.Geo.Record.Record method)
(Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment method)
(Bio.Graphics.BasicChromosome.Chromosome method)
(Bio.Graphics.BasicChromosome.ChromosomeSegment method)
(Bio.Graphics.BasicChromosome.Organism method)
(Bio.Graphics.BasicChromosome.TelomereSegment method)
(Bio.Graphics.ColorSpiral.ColorSpiral method)
(Bio.Graphics.Comparative.ComparativeScatterPlot method)
(Bio.Graphics.DisplayRepresentation.ChromosomeCounts method)
(Bio.Graphics.Distribution.BarChartDistribution method)
(Bio.Graphics.Distribution.DistributionPage method)
(Bio.Graphics.Distribution.LineDistribution method)
(Bio.Graphics.GenomeDiagram.ColorTranslator method)
(Bio.Graphics.GenomeDiagram.CrossLink method)
(Bio.Graphics.GenomeDiagram.Diagram method)
(Bio.Graphics.GenomeDiagram.Feature method)
(Bio.Graphics.GenomeDiagram.FeatureSet method)
(Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.Graphics.GenomeDiagram.GraphSet method)
(Bio.Graphics.GenomeDiagram.Track method)
(Bio.Graphics.KGML_vis.KGMLCanvas method)
(Bio.HMM.DynamicProgramming.AbstractDPAlgorithms method)
(Bio.HMM.DynamicProgramming.LogDPAlgorithms method)
(Bio.HMM.DynamicProgramming.ScaledDPAlgorithms method)
(Bio.HMM.MarkovModel.HiddenMarkovModel method)
(Bio.HMM.MarkovModel.MarkovModelBuilder method)
(Bio.HMM.Trainer.AbstractTrainer method)
(Bio.HMM.Trainer.BaumWelchTrainer method)
(Bio.HMM.Trainer.KnownStateTrainer method)
(Bio.HMM.Trainer.TrainingSequence method)
(Bio.KEGG.Compound.Record method)
(Bio.KEGG.Enzyme.Record method)
(Bio.KEGG.Gene.Record method)
(Bio.KEGG.KGML.KGML_parser.KGMLParser method)
(Bio.KEGG.KGML.KGML_pathway.Component method)
(Bio.KEGG.KGML.KGML_pathway.Entry method)
(Bio.KEGG.KGML.KGML_pathway.Graphics method)
(Bio.KEGG.KGML.KGML_pathway.Pathway method)
(Bio.KEGG.KGML.KGML_pathway.Reaction method)
(Bio.KEGG.KGML.KGML_pathway.Relation method)
(Bio.kNN.kNN method)
(Bio.LogisticRegression.LogisticRegression method)
(Bio.MarkovModel.MarkovModel method)
(Bio.MaxEntropy.MaxEntropy method)
(Bio.motifs.alignace.Record method)
(Bio.motifs.Instances method)
(Bio.motifs.jaspar.db.JASPAR5 method)
(Bio.motifs.jaspar.Motif method)
(Bio.motifs.jaspar.Record method)
(Bio.motifs.mast.Record method)
(Bio.motifs.matrix.GenericPositionMatrix method)
(Bio.motifs.matrix.PositionWeightMatrix method)
(Bio.motifs.meme.Instance method)
(Bio.motifs.meme.Motif method)
(Bio.motifs.meme.Record method)
(Bio.motifs.minimal.Record method)
(Bio.motifs.Motif method)
(Bio.motifs.thresholds.ScoreDistribution method)
(Bio.motifs.transfac.Record method)
(Bio.motifs.xms.XMSScanner method)
(Bio.NaiveBayes.NaiveBayes method)
(Bio.Nexus.Nexus.Block method)
(Bio.Nexus.Nexus.CharBuffer method)
(Bio.Nexus.Nexus.Commandline method)
(Bio.Nexus.Nexus.Nexus method)
(Bio.Nexus.Nexus.StepMatrix method)
(Bio.Nexus.Nodes.Chain method)
(Bio.Nexus.Nodes.Node method)
(Bio.Nexus.StandardData.StandardData method)
(Bio.Nexus.Trees.NodeData method)
(Bio.Nexus.Trees.Tree method)
(Bio.NMR.xpktools.Peaklist method)
(Bio.NMR.xpktools.XpkEntry method)
(Bio.pairwise2.affine_penalty method)
(Bio.pairwise2.dictionary_match method)
(Bio.pairwise2.identity_match method)
(Bio.Pathway.Network method)
(Bio.Pathway.Reaction method)
(Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
(Bio.Pathway.System method)
(Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap method)
(Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method)
(Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Atom.DisorderedAtom method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Dice.ChainSelector method)
(Bio.PDB.DSSP.DSSP method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.FragmentMapper.Fragment method)
(Bio.PDB.FragmentMapper.FragmentMapper method)
(Bio.PDB.HSExposure.ExposureCN method)
(Bio.PDB.HSExposure.HSExposureCA method)
(Bio.PDB.HSExposure.HSExposureCB method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.Dihedron method)
(Bio.PDB.internal_coords.Edron method)
(Bio.PDB.internal_coords.Hedron method)
(Bio.PDB.internal_coords.IC_Chain method)
(Bio.PDB.internal_coords.IC_Residue method)
(Bio.PDB.MMCIF2Dict.MMCIF2Dict method)
(Bio.PDB.mmcifio.MMCIFIO method)
(Bio.PDB.MMCIFParser.FastMMCIFParser method)
(Bio.PDB.MMCIFParser.MMCIFParser method)
(Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
(Bio.PDB.mmtf.mmtfio.MMTFIO method)
(Bio.PDB.Model.Model method)
(Bio.PDB.NACCESS.NACCESS method)
(Bio.PDB.NACCESS.NACCESS_atomic method)
(Bio.PDB.NeighborSearch.NeighborSearch method)
(Bio.PDB.PDBIO.PDBIO method)
(Bio.PDB.PDBIO.StructureIO method)
(Bio.PDB.PDBList.PDBList method)
(Bio.PDB.PDBParser.PDBParser method)
(Bio.PDB.Polypeptide.CaPPBuilder method)
(Bio.PDB.Polypeptide.PPBuilder method)
(Bio.PDB.PSEA.PSEA method)
(Bio.PDB.QCPSuperimposer.QCPSuperimposer method)
(Bio.PDB.Residue.DisorderedResidue method)
(Bio.PDB.Residue.Residue method)
(Bio.PDB.ResidueDepth.ResidueDepth method)
(Bio.PDB.Structure.Structure method)
(Bio.PDB.StructureAlignment.StructureAlignment method)
(Bio.PDB.StructureBuilder.StructureBuilder method)
(Bio.PDB.Superimposer.Superimposer method)
(Bio.PDB.vectors.Vector method)
(Bio.phenotype.phen_micro.JsonWriter method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.Applications.FastTreeCommandline method)
(Bio.Phylo.Applications.PhymlCommandline method)
(Bio.Phylo.Applications.RaxmlCommandline method)
(Bio.Phylo.BaseTree.BranchColor method)
(Bio.Phylo.BaseTree.Clade method)
(Bio.Phylo.BaseTree.Tree method)
(Bio.Phylo.CDAO.Clade method)
(Bio.Phylo.CDAO.Tree method)
(Bio.Phylo.CDAOIO.Parser method)
(Bio.Phylo.CDAOIO.Writer method)
(Bio.Phylo.Newick.Clade method)
(Bio.Phylo.Newick.Tree method)
(Bio.Phylo.NewickIO.Parser method)
(Bio.Phylo.NewickIO.Writer method)
(Bio.Phylo.NeXML.Clade method)
(Bio.Phylo.NeXML.Tree method)
(Bio.Phylo.NeXMLIO.Parser method)
(Bio.Phylo.NeXMLIO.Writer method)
(Bio.Phylo.PAML.baseml.Baseml method)
(Bio.Phylo.PAML.codeml.Codeml method)
(Bio.Phylo.PAML.yn00.Yn00 method)
(Bio.Phylo.PhyloXML.Accession method)
(Bio.Phylo.PhyloXML.Annotation method)
(Bio.Phylo.PhyloXML.BinaryCharacters method)
(Bio.Phylo.PhyloXML.BranchColor method)
(Bio.Phylo.PhyloXML.Clade method)
(Bio.Phylo.PhyloXML.CladeRelation method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Phylo.PhyloXML.Date method)
(Bio.Phylo.PhyloXML.Distribution method)
(Bio.Phylo.PhyloXML.DomainArchitecture method)
(Bio.Phylo.PhyloXML.Events method)
(Bio.Phylo.PhyloXML.Id method)
(Bio.Phylo.PhyloXML.MolSeq method)
(Bio.Phylo.PhyloXML.Other method)
(Bio.Phylo.PhyloXML.Phylogeny method)
(Bio.Phylo.PhyloXML.Phyloxml method)
(Bio.Phylo.PhyloXML.Point method)
(Bio.Phylo.PhyloXML.Polygon method)
(Bio.Phylo.PhyloXML.Property method)
(Bio.Phylo.PhyloXML.ProteinDomain method)
(Bio.Phylo.PhyloXML.Reference method)
(Bio.Phylo.PhyloXML.Sequence method)
(Bio.Phylo.PhyloXML.SequenceRelation method)
(Bio.Phylo.PhyloXML.Taxonomy method)
(Bio.Phylo.PhyloXML.Uri method)
(Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
(Bio.Phylo.TreeConstruction.DistanceCalculator method)
(Bio.Phylo.TreeConstruction.DistanceMatrix method)
(Bio.Phylo.TreeConstruction.DistanceTreeConstructor method)
(Bio.Phylo.TreeConstruction.NNITreeSearcher method)
(Bio.Phylo.TreeConstruction.ParsimonyScorer method)
(Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor method)
(Bio.PopGen.GenePop.Controller.GenePopController method)
(Bio.PopGen.GenePop.EasyController.EasyController method)
(Bio.PopGen.GenePop.FileParser.FileRecord method)
(Bio.PopGen.GenePop.LargeFileParser.Record method)
(Bio.PopGen.GenePop.Record method)
(Bio.SCOP.Astral method)
(Bio.SCOP.Cla.Index method)
(Bio.SCOP.Cla.Record method)
(Bio.SCOP.Des.Record method)
(Bio.SCOP.Dom.Record method)
(Bio.SCOP.Domain method)
(Bio.SCOP.Hie.Record method)
(Bio.SCOP.Node method)
(Bio.SCOP.Raf.Res method)
(Bio.SCOP.Raf.SeqMap method)
(Bio.SCOP.Raf.SeqMapIndex method)
(Bio.SCOP.Residues.Residues method)
(Bio.SCOP.Scop method)
(Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer method)
(Bio.SearchIO.BlastIO.blast_tab.BlastTabParser method)
(Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter method)
(Bio.SearchIO.BlastIO.blast_text.BlastTextParser method)
(Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer method)
(Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser method)
(Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter method)
(Bio.SearchIO.BlatIO.BlatPslIndexer method)
(Bio.SearchIO.BlatIO.BlatPslParser method)
(Bio.SearchIO.BlatIO.BlatPslWriter method)
(Bio.SearchIO.FastaIO.FastaM10Indexer method)
(Bio.SearchIO.FastaIO.FastaM10Parser method)
(Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser method)
(Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
(Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter method)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser method)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter method)
(Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser method)
(Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqFeature.PositionGap method)
(Bio.SeqFeature.Reference method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqIO.AbiIO.AbiIterator method)
(Bio.SeqIO.FastaIO.FastaIterator method)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)
(Bio.SeqIO.FastaIO.FastaTwoLineWriter method)
(Bio.SeqIO.FastaIO.FastaWriter method)
(Bio.SeqIO.GckIO.GckIterator method)
(Bio.SeqIO.IgIO.IgIterator method)
(Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator method)
(Bio.SeqIO.InsdcIO.EmblIterator method)
(Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator method)
(Bio.SeqIO.InsdcIO.GenBankIterator method)
(Bio.SeqIO.InsdcIO.ImgtIterator method)
(Bio.SeqIO.Interfaces.SequenceIterator method)
(Bio.SeqIO.Interfaces.SequenceWriter method)
(Bio.SeqIO.Interfaces.SequentialSequenceWriter method)
(Bio.SeqIO.NibIO.NibIterator method)
(Bio.SeqIO.NibIO.NibWriter method)
(Bio.SeqIO.PdbIO.PdbSeqresIterator method)
(Bio.SeqIO.PhdIO.PhdWriter method)
(Bio.SeqIO.PirIO.PirIterator method)
(Bio.SeqIO.PirIO.PirWriter method)
(Bio.SeqIO.QualityIO.FastqPhredIterator method)
(Bio.SeqIO.QualityIO.QualPhredIterator method)
(Bio.SeqIO.QualityIO.QualPhredWriter method)
(Bio.SeqIO.SeqXmlIO.ContentHandler method)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator method)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter method)
(Bio.SeqIO.SffIO.SffIterator method)
(Bio.SeqIO.SffIO.SffWriter method)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator method)
(Bio.SeqIO.TabIO.TabIterator method)
(Bio.SeqIO.UniprotIO.Parser method)
(Bio.SeqIO.XdnaIO.XdnaIterator method)
(Bio.SeqIO.XdnaIO.XdnaWriter method)
(Bio.SeqRecord.SeqRecord method)
(Bio.Sequencing.Ace.ACEFileRecord method)
(Bio.Sequencing.Ace.af method)
(Bio.Sequencing.Ace.bs method)
(Bio.Sequencing.Ace.Contig method)
(Bio.Sequencing.Ace.ct method)
(Bio.Sequencing.Ace.ds method)
(Bio.Sequencing.Ace.qa method)
(Bio.Sequencing.Ace.rd method)
(Bio.Sequencing.Ace.Reads method)
(Bio.Sequencing.Ace.rt method)
(Bio.Sequencing.Ace.wa method)
(Bio.Sequencing.Ace.wr method)
(Bio.Sequencing.Applications.BwaAlignCommandline method)
(Bio.Sequencing.Applications.BwaBwaswCommandline method)
(Bio.Sequencing.Applications.BwaIndexCommandline method)
(Bio.Sequencing.Applications.BwaMemCommandline method)
(Bio.Sequencing.Applications.BwaSampeCommandline method)
(Bio.Sequencing.Applications.BwaSamseCommandline method)
(Bio.Sequencing.Applications.NovoalignCommandline method)
(Bio.Sequencing.Applications.SamtoolsCalmdCommandline method)
(Bio.Sequencing.Applications.SamtoolsCatCommandline method)
(Bio.Sequencing.Applications.SamtoolsFaidxCommandline method)
(Bio.Sequencing.Applications.SamtoolsFixmateCommandline method)
(Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline method)
(Bio.Sequencing.Applications.SamtoolsIndexCommandline method)
(Bio.Sequencing.Applications.SamtoolsMergeCommandline method)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline method)
(Bio.Sequencing.Applications.SamtoolsPhaseCommandline method)
(Bio.Sequencing.Applications.SamtoolsReheaderCommandline method)
(Bio.Sequencing.Applications.SamtoolsRmdupCommandline method)
(Bio.Sequencing.Applications.SamtoolsTargetcutCommandline method)
(Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline method)
(Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline method)
(Bio.Sequencing.Applications.SamtoolsViewCommandline method)
(Bio.Sequencing.Phd.Record method)
(Bio.SeqUtils.CodonUsage.CodonAdaptationIndex method)
(Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint method)
(Bio.SeqUtils.ProtParam.ProteinAnalysis method)
(Bio.SubsMat.FreqTable.FreqTable method)
(Bio.SubsMat.SeqMat method)
(Bio.SVDSuperimposer.SVDSuperimposer method)
(Bio.SwissProt.KeyWList.Record method)
(Bio.SwissProt.Record method)
(Bio.SwissProt.Reference method)
(Bio.SwissProt.SwissProtParserError method)
(Bio.UniGene.ProtsimLine method)
(Bio.UniGene.Record method)
(Bio.UniGene.SequenceLine method)
(Bio.UniGene.STSLine method)
(Bio.Wise.dnal.Statistics method)
(Bio.Wise.psw.AlignmentColumn method)
(Bio.Wise.psw.ColumnUnit method)
(BioSQL.BioSeq.DBSeq method)
(BioSQL.BioSeq.DBSeqRecord method)
(BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
(BioSQL.DBUtils.Generic_dbutils method)
(BioSQL.Loader.DatabaseLoader method)
(BioSQL.Loader.DatabaseRemover method)
__int__() (Bio.Phylo.PhyloXML.Confidence method)
__iter__() (Bio.Align.MultipleSeqAlignment method)
(Bio.Align.PairwiseAlignments method)
(Bio.AlignIO.Interfaces.AlignmentIterator method)
(Bio.bgzf.BgzfReader method)
(Bio.GenBank.Iterator method)
(Bio.Nexus.StandardData.StandardData method)
(Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method)
(Bio.PDB.Atom.DisorderedAtom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.BaseTree.Clade method)
(Bio.Phylo.PhyloXML.Events method)
(Bio.Phylo.PhyloXML.Other method)
(Bio.Phylo.PhyloXML.Phyloxml method)
(Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer method)
(Bio.SearchIO.BlastIO.blast_tab.BlastTabParser method)
(Bio.SearchIO.BlastIO.blast_text.BlastTextParser method)
(Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer method)
(Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser method)
(Bio.SearchIO.BlatIO.BlatPslIndexer method)
(Bio.SearchIO.BlatIO.BlatPslParser method)
(Bio.SearchIO.FastaIO.FastaM10Indexer method)
(Bio.SearchIO.FastaIO.FastaM10Parser method)
(Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser method)
(Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer method)
(Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer method)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser method)
(Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer method)
(Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser method)
(Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqIO.Interfaces.SequenceIterator method)
(Bio.SeqRecord.SeqRecord method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
__le__() (Bio.Align.PairwiseAlignment method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.Edron method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
__le___() (Bio.SeqRecord.SeqRecord method)
__len__() (Bio.Align.MultipleSeqAlignment method)
(Bio.Align.PairwiseAlignments method)
(Bio.AlignIO.MafIO.MafIndex method)
(Bio.Crystal.Chain method)
(Bio.Crystal.Crystal method)
(Bio.Crystal.Hetero method)
(Bio.Emboss.Primer3.Primers method)
(Bio.FSSP.fssp_rec.fff_rec method)
(Bio.Graphics.GenomeDiagram.FeatureSet method)
(Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.Graphics.GenomeDiagram.GraphSet method)
(Bio.motifs.Motif method)
(Bio.Nexus.StandardData.StandardData method)
(Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.FragmentMapper.Fragment method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.BaseTree.Clade method)
(Bio.Phylo.PhyloXML.Events method)
(Bio.Phylo.PhyloXML.Phyloxml method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqRecord.SeqRecord method)
(BioSQL.BioSeq.DBSeq method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
__lt__() (Bio.Align.PairwiseAlignment method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.Edron method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.SeqRecord.SeqRecord method)
__mod__() (Bio.Phylo.PhyloXML.Confidence method)
__mul__() (Bio.PDB.vectors.Vector method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SubsMat.SeqMat method)
(BioSQL.BioSeq.DBSeq method)
__ne__() (Bio.Align.PairwiseAlignment method)
(Bio.Crystal.Chain method)
(Bio.Entrez.Parser.NoneElement method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.Edron method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.SeqRecord.SeqRecord method)
__neg__() (Bio.PDB.vectors.Vector method)
(Bio.Phylo.PhyloXML.Confidence method)
__new__() (Bio.Align.substitution_matrices.Array static method)
(Bio.Entrez.Parser.IntegerElement static method)
(Bio.Entrez.Parser.StringElement static method)
(Bio.PDB.internal_coords.AtomKey.fieldsDef static method)
(Bio.SeqFeature.AfterPosition static method)
(Bio.SeqFeature.BeforePosition static method)
(Bio.SeqFeature.BetweenPosition static method)
(Bio.SeqFeature.ExactPosition static method)
(Bio.SeqFeature.OneOfPosition static method)
(Bio.SeqFeature.WithinPosition static method)
__next__() (Bio.Align.PairwiseAlignments method)
(Bio.AlignIO.ClustalIO.ClustalIterator method)
(Bio.AlignIO.EmbossIO.EmbossIterator method)
(Bio.AlignIO.Interfaces.AlignmentIterator method)
(Bio.AlignIO.MauveIO.MauveIterator method)
(Bio.AlignIO.MsfIO.MsfIterator method)
(Bio.AlignIO.PhylipIO.PhylipIterator method)
(Bio.AlignIO.PhylipIO.SequentialPhylipIterator method)
(Bio.AlignIO.StockholmIO.StockholmIterator method)
(Bio.bgzf.BgzfReader method)
(Bio.Blast.ParseBlastTable.BlastTableReader method)
(Bio.GenBank.Iterator method)
(Bio.Nexus.Nexus.CharBuffer method)
(Bio.Nexus.StandardData.StandardData method)
(Bio.SeqIO.Interfaces.SequenceIterator method)
__nonzero__() (Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
__pos__() (Bio.Phylo.PhyloXML.Confidence method)
__pow__() (Bio.PDB.vectors.Vector method)
(Bio.Phylo.PhyloXML.Confidence method)
__radd__() (Bio.Crystal.Chain method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqRecord.SeqRecord method)
(BioSQL.BioSeq.DBSeq method)
__rdivmod__() (Bio.Phylo.PhyloXML.Confidence method)
__repr__() (Bio.Align.MultipleSeqAlignment method)
(Bio.Align.substitution_matrices.Array method)
(Bio.AlignIO.MafIO.MafIndex method)
(Bio.Application.AbstractCommandline method)
(Bio.Application.ApplicationError method)
(Bio.Crystal.Crystal method)
(Bio.Crystal.Hetero method)
(Bio.Data.CodonTable.NCBICodonTable method)
(Bio.Entrez.Parser.DictionaryElement method)
(Bio.Entrez.Parser.IntegerElement method)
(Bio.Entrez.Parser.ListElement method)
(Bio.Entrez.Parser.NoneElement method)
(Bio.Entrez.Parser.StringElement method)
(Bio.ExPASy.cellosaurus.Record method)
(Bio.ExPASy.Enzyme.Record method)
(Bio.FSSP.fssp_rec.fff_rec method)
(Bio.FSSP.FSSPSumRec method)
(Bio.FSSP.PosAlign method)
(Bio.GenBank.Record.Feature method)
(Bio.GenBank.Record.Qualifier method)
(Bio.GenBank.utils.FeatureValueCleaner method)
(Bio.Pathway.Interaction method)
(Bio.Pathway.Network method)
(Bio.Pathway.Reaction method)
(Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
(Bio.Pathway.System method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Atom.DisorderedAtom method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.FragmentMapper.Fragment method)
(Bio.PDB.internal_coords.AtomKey method)
(Bio.PDB.internal_coords.AtomKey.fieldsDef method)
(Bio.PDB.internal_coords.Dihedron method)
(Bio.PDB.internal_coords.Edron method)
(Bio.PDB.internal_coords.Hedron method)
(Bio.PDB.internal_coords.IC_Residue method)
(Bio.PDB.Model.Model method)
(Bio.PDB.PDBIO.Select method)
(Bio.PDB.Polypeptide.Polypeptide method)
(Bio.PDB.Residue.DisorderedResidue method)
(Bio.PDB.Residue.Residue method)
(Bio.PDB.Structure.Structure method)
(Bio.PDB.vectors.Vector method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.BaseTree.BranchColor method)
(Bio.Phylo.BaseTree.TreeElement method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqFeature.AbstractPosition method)
(Bio.SeqFeature.AfterPosition method)
(Bio.SeqFeature.BeforePosition method)
(Bio.SeqFeature.BetweenPosition method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.ExactPosition method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqFeature.OneOfPosition method)
(Bio.SeqFeature.PositionGap method)
(Bio.SeqFeature.Reference method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqFeature.UnknownPosition method)
(Bio.SeqFeature.WithinPosition method)
(Bio.SeqRecord.SeqRecord method)
(Bio.UniGene.ProtsimLine method)
(Bio.UniGene.Record method)
(Bio.UniGene.SequenceLine method)
(Bio.UniGene.STSLine method)
(Bio.Wise.psw.AlignmentColumn method)
(Bio.Wise.psw.ColumnUnit method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
__rfloordiv__() (Bio.Phylo.PhyloXML.Confidence method)
__rmod__() (Bio.Phylo.PhyloXML.Confidence method)
__rmul__() (Bio.Phylo.PhyloXML.Confidence method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SubsMat.SeqMat method)
(BioSQL.BioSeq.DBSeq method)
__rpow__() (Bio.Phylo.PhyloXML.Confidence method)
__rsub__() (Bio.Phylo.PhyloXML.Confidence method)
__rtruediv__() (Bio.Phylo.PhyloXML.Confidence method)
__setattr__() (Bio.Align.PairwiseAligner method)
(Bio.Application.AbstractCommandline method)
__setitem__() (Bio.Align.substitution_matrices.Array method)
(Bio.Crystal.Chain method)
(Bio.Crystal.Crystal method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.vectors.Vector method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.PhyloXML.Events method)
(Bio.Phylo.TreeConstruction.DistanceMatrix method)
(Bio.Seq.MutableSeq method)
__slots__ (Bio.PDB.internal_coords.AtomKey.fieldsDef attribute)
__str__() (Bio.Align.AlignInfo.PSSM method)
(Bio.Align.MultipleSeqAlignment method)
(Bio.Align.PairwiseAlignment method)
(Bio.Align.substitution_matrices.Array method)
(Bio.Application.AbstractCommandline method)
(Bio.Application.ApplicationError method)
(Bio.Blast.Record.Alignment method)
(Bio.Blast.Record.Description method)
(Bio.Blast.Record.DescriptionExtItem method)
(Bio.Blast.Record.HSP method)
(Bio.codonalign.codonalignment.CodonAlignment method)
(Bio.Crystal.Chain method)
(Bio.Crystal.Crystal method)
(Bio.Crystal.Hetero method)
(Bio.Data.CodonTable.CodonTable method)
(Bio.Emboss.PrimerSearch.InputRecord method)
(Bio.Entrez.Parser.CorruptedXMLError method)
(Bio.Entrez.Parser.NotXMLError method)
(Bio.Entrez.Parser.ValidationError method)
(Bio.ExPASy.cellosaurus.Record method)
(Bio.ExPASy.Enzyme.Record method)
(Bio.GenBank.Record.Feature method)
(Bio.GenBank.Record.Qualifier method)
(Bio.GenBank.Record.Record method)
(Bio.GenBank.Record.Reference method)
(Bio.Geo.Record.Record method)
(Bio.Graphics.GenomeDiagram.Diagram method)
(Bio.Graphics.GenomeDiagram.FeatureSet method)
(Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.Graphics.GenomeDiagram.GraphSet method)
(Bio.Graphics.GenomeDiagram.Track method)
(Bio.KEGG.Compound.Record method)
(Bio.KEGG.Enzyme.Record method)
(Bio.KEGG.Gene.Record method)
(Bio.KEGG.KGML.KGML_pathway.Entry method)
(Bio.KEGG.KGML.KGML_pathway.Pathway method)
(Bio.KEGG.KGML.KGML_pathway.Reaction method)
(Bio.KEGG.KGML.KGML_pathway.Relation method)
(Bio.MarkovModel.MarkovModel method)
(Bio.motifs.clusterbuster.Record method)
(Bio.motifs.Instances method)
(Bio.motifs.jaspar.db.JASPAR5 method)
(Bio.motifs.jaspar.Motif method)
(Bio.motifs.jaspar.Record method)
(Bio.motifs.matrix.GenericPositionMatrix method)
(Bio.motifs.Motif method)
(Bio.motifs.pfm.Record method)
(Bio.motifs.transfac.Record method)
(Bio.motifs.xms.Record method)
(Bio.Nexus.StandardData.StandardData method)
(Bio.Nexus.Trees.Tree method)
(Bio.Pathway.Interaction method)
(Bio.Pathway.Network method)
(Bio.Pathway.Reaction method)
(Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
(Bio.Pathway.System method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.BaseTree.BranchColor method)
(Bio.Phylo.BaseTree.Clade method)
(Bio.Phylo.BaseTree.Tree method)
(Bio.Phylo.BaseTree.TreeElement method)
(Bio.Phylo.PhyloXML.Accession method)
(Bio.Phylo.PhyloXML.Date method)
(Bio.Phylo.PhyloXML.Id method)
(Bio.Phylo.PhyloXML.MolSeq method)
(Bio.Phylo.PhyloXML.Phyloxml method)
(Bio.Phylo.PhyloXML.Polygon method)
(Bio.Phylo.PhyloXML.Taxonomy method)
(Bio.Phylo.PhyloXML.Uri method)
(Bio.PopGen.GenePop.FileParser.FileRecord method)
(Bio.PopGen.GenePop.Record method)
(Bio.SCOP.Cla.Record method)
(Bio.SCOP.Des.Record method)
(Bio.SCOP.Dom.Record method)
(Bio.SCOP.Domain method)
(Bio.SCOP.Hie.Record method)
(Bio.SCOP.Node method)
(Bio.SCOP.Residues.Residues method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqFeature.AfterPosition method)
(Bio.SeqFeature.BeforePosition method)
(Bio.SeqFeature.BetweenPosition method)
(Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.ExactPosition method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqFeature.OneOfPosition method)
(Bio.SeqFeature.PositionGap method)
(Bio.SeqFeature.Reference method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqFeature.WithinPosition method)
(Bio.SeqRecord.SeqRecord method)
(Bio.SubsMat.SeqMat method)
(Bio.Wise.dnal.Statistics method)
(BioSQL.BioSeq.DBSeq method)
__sub__() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.FragmentMapper.Fragment method)
(Bio.PDB.vectors.Vector method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.phenotype.phen_micro.WellRecord method)
(Bio.Phylo.PhyloXML.Confidence method)
(Bio.SubsMat.SeqMat method)
__truediv__() (Bio.PDB.vectors.Vector method)
(Bio.Phylo.PhyloXML.Confidence method)
A
a() (Bio.Align.Applications.ProbconsCommandline property)
(Bio.Graphics.ColorSpiral.ColorSpiral property)
(Bio.Sequencing.Applications.BwaBwaswCommandline property)
A() (Bio.Sequencing.Applications.BwaMemCommandline property)
a() (Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.BwaSampeCommandline property)
A() (Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
(Bio.Sequencing.Applications.SamtoolsPhaseCommandline property)
aacateg() (Bio.Emboss.Applications.FProtDistCommandline property)
aamatrix() (Bio.Align.Applications.MafftCommandline property)
AbiIterator (class in Bio.SeqIO.AbiIO)
abs() (Bio.FSSP.FSSPAlignDict method)
abs_res_num (Bio.FSSP.fssp_rec.align attribute)
AbstractAtomPropertyMap (class in Bio.PDB.AbstractPropertyMap)
AbstractCommandline (class in Bio.Application)
AbstractDPAlgorithms (class in Bio.HMM.DynamicProgramming)
AbstractPosition (class in Bio.SeqFeature)
AbstractPropertyMap (class in Bio.PDB.AbstractPropertyMap)
AbstractResiduePropertyMap (class in Bio.PDB.AbstractPropertyMap)
AbstractTrainer (class in Bio.HMM.Trainer)
acc (Bio.FSSP.fssp_rec.align attribute)
accept_atom() (Bio.PDB.Dice.ChainSelector method)
(Bio.PDB.PDBIO.Select method)
accept_atoms (Bio.PDB.internal_coords.IC_Residue attribute)
accept_chain() (Bio.PDB.Dice.ChainSelector method)
(Bio.PDB.PDBIO.Select method)
accept_deuteriums (Bio.PDB.internal_coords.IC_Residue attribute)
accept_hydrogens (Bio.PDB.internal_coords.IC_Residue attribute)
accept_mainchain (Bio.PDB.internal_coords.IC_Residue attribute)
accept_model() (Bio.PDB.Dice.ChainSelector method)
(Bio.PDB.PDBIO.Select method)
accept_residue() (Bio.PDB.Dice.ChainSelector method)
(Bio.PDB.PDBIO.Select method)
accept_resnames (Bio.PDB.internal_coords.IC_Residue attribute)
Accession (class in Bio.Phylo.PhyloXML)
accession() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
ACEFileRecord (class in Bio.Sequencing.Ace)
AceIterator() (in module Bio.SeqIO.AceIO)
adam_consensus() (in module Bio.Phylo.Consensus)
adapter3() (Bio.Sequencing.Applications.NovoalignCommandline property)
adapter5() (Bio.Sequencing.Applications.NovoalignCommandline property)
Adaptor (class in BioSQL.BioSeqDatabase)
add() (Bio.Nexus.Nexus.StepMatrix method)
(Bio.Nexus.Nodes.Chain method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.Residue.DisorderedResidue method)
(Bio.PDB.Residue.Residue method)
add_align_list() (Bio.FSSP.FSSPAlignRec method)
add_annotation() (Bio.Phylo.NeXMLIO.Parser method)
add_component() (Bio.KEGG.KGML.KGML_pathway.Entry method)
add_count() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method)
add_edge() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
add_entry() (Bio.Blast.ParseBlastTable.BlastTableRec method)
(Bio.KEGG.KGML.KGML_pathway.Pathway method)
add_feature() (Bio.Graphics.GenomeDiagram.FeatureSet method)
add_graphics() (Bio.KEGG.KGML.KGML_pathway.Entry method)
add_interaction() (Bio.Pathway.Network method)
add_label() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method)
add_node() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
add_point() (Bio.Graphics.GenomeDiagram.GraphData method)
add_primer_set() (Bio.Emboss.PrimerSearch.InputRecord method)
add_product() (Bio.KEGG.KGML.KGML_pathway.Reaction method)
add_reaction() (Bio.KEGG.KGML.KGML_pathway.Pathway method)
(Bio.Pathway.System method)
add_relation() (Bio.KEGG.KGML.KGML_pathway.Pathway method)
add_residue() (Bio.PDB.FragmentMapper.Fragment method)
add_sequence() (Bio.Align.MultipleSeqAlignment method)
(Bio.Nexus.Nexus.Nexus method)
add_set() (Bio.Graphics.GenomeDiagram.Track method)
add_species() (Bio.Pathway.Network method)
add_stmt_to_handle() (Bio.Phylo.CDAOIO.Writer method)
add_substrate() (Bio.KEGG.KGML.KGML_pathway.Reaction method)
add_succ() (Bio.Nexus.Nodes.Node method)
add_track() (Bio.Graphics.GenomeDiagram.Diagram method)
adjustdirection() (Bio.Align.Applications.MafftCommandline property)
adjustdirectionaccurately() (Bio.Align.Applications.MafftCommandline property)
af (class in Bio.Sequencing.Ace)
afc() (Bio.Align.Applications.DialignCommandline property)
afc_v() (Bio.Align.Applications.DialignCommandline property)
affine_penalty (class in Bio.pairwise2)
aformat() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
AfterPosition (class in Bio.SeqFeature)
algorithm() (Bio.Phylo.Applications.RaxmlCommandline property)
(Bio.Sequencing.Applications.BwaIndexCommandline property)
align (class in Bio.FSSP.fssp_rec)
align() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.PairwiseAligner method)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(in module Bio.Wise)
(in module Bio.Wise.dnal)
(in module Bio.Wise.psw)
aligned() (Bio.Align.PairwiseAlignment property)
Alignment (class in Bio.Blast.Record)
(class in Bio.Wise.psw)
alignment_order() (Bio.Align.Applications.MSAProbsCommandline property)
AlignmentColumn (class in Bio.Wise.psw)
AlignmentColumnFullException
AlignmentHasDifferentLengthsError
AlignmentIterator (class in Bio.AlignIO.Interfaces)
AlignmentWriter (class in Bio.AlignIO.Interfaces)
all_ids() (Bio.Nexus.Nodes.Chain method)
all_pairs() (in module Bio.Wise)
AllBonds (Bio.PDB.internal_coords.IC_Residue attribute)
allow_all_transitions() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
allow_transition() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
alpha() (Bio.Phylo.Applications.PhymlCommandline property)
alphabet() (Bio.Align.substitution_matrices.Array property)
alt() (Bio.Phylo.PhyloXMLIO.Writer method)
altloc() (Bio.PDB.internal_coords.AtomKey.fieldsDef property)
altloc_match() (Bio.PDB.internal_coords.AtomKey method)
AmbiguousCodonTable (class in Bio.Data.CodonTable)
AmbiguousForwardTable (class in Bio.Data.CodonTable)
amino() (Bio.Align.Applications.MafftCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
Amplifier (class in Bio.Emboss.PrimerSearch)
anc() (Bio.Align.Applications.DialignCommandline property)
anchors() (Bio.Align.Applications.MuscleCommandline property)
anchorspacing() (Bio.Align.Applications.MuscleCommandline property)
angle() (Bio.PDB.internal_coords.Dihedron property)
(Bio.PDB.internal_coords.Hedron property)
(Bio.PDB.vectors.Vector method)
annot() (Bio.Align.Applications.MSAProbsCommandline property)
(Bio.Align.Applications.ProbconsCommandline property)
annotate() (in module Bio.PDB.PSEA)
AnnotatedChromosomeSegment (class in Bio.Graphics.BasicChromosome)
Annotation (class in Bio.Phylo.PhyloXML)
annotation() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
annotations() (BioSQL.BioSeq.DBSeqRecord property)
anticonsensus() (Bio.motifs.matrix.GenericPositionMatrix property)
(Bio.motifs.Motif property)
aoutfeat() (Bio.Emboss.Applications.DiffseqCommandline property)
append() (Bio.Align.MultipleSeqAlignment method)
(Bio.Crystal.Chain method)
(Bio.SCOP.Raf.SeqMap method)
(Bio.Seq.MutableSeq method)
(Bio.Wise.psw.Alignment method)
(Bio.Wise.psw.AlignmentColumn method)
append_item() (Bio.Blast.Record.DescriptionExt method)
append_sets() (Bio.Nexus.Nexus.Nexus method)
ApplicationError
apply() (Bio.PDB.Superimposer.Superimposer method)
applyMtx() (Bio.PDB.internal_coords.IC_Residue method)
archive() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
aromaticity() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
Array (class in Bio.Align.substitution_matrices)
artemis_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method)
as_fasta() (in module Bio.SeqIO.FastaIO)
as_fasta_2line() (in module Bio.SeqIO.FastaIO)
as_fastq() (in module Bio.SeqIO.QualityIO)
as_fastq_illumina() (in module Bio.SeqIO.QualityIO)
as_fastq_solexa() (in module Bio.SeqIO.QualityIO)
as_handle() (in module Bio.File)
as_phyloxml() (Bio.Phylo.BaseTree.Tree method)
(Bio.Phylo.PhyloXML.Phylogeny method)
as_qual() (in module Bio.SeqIO.QualityIO)
as_tab() (in module Bio.SeqIO.TabIO)
asequence() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
assemble() (Bio.PDB.internal_coords.IC_Residue method)
assemble_residues() (Bio.PDB.internal_coords.IC_Chain method)
Astral (class in Bio.SCOP)
atm() (Bio.PDB.internal_coords.AtomKey.fieldsDef property)
atm241() (Bio.PDB.internal_coords.IC_Residue static method)
Atom (class in Bio.PDB.Atom)
atom_re (Bio.PDB.internal_coords.AtomKey attribute)
atom_to_internal_coordinates() (Bio.PDB.Chain.Chain method)
(Bio.PDB.internal_coords.IC_Chain method)
(Bio.PDB.internal_coords.IC_Residue method)
(Bio.PDB.Model.Model method)
(Bio.PDB.Structure.Structure method)
AtomIterator() (in module Bio.SeqIO.PdbIO)
AtomKey (class in Bio.PDB.internal_coords)
AtomKey.fieldsDef (class in Bio.PDB.internal_coords)
auto() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.MafftCommandline property)
(Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
autocommit() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.DBUtils.Generic_dbutils method)
(BioSQL.DBUtils.Pgdb_dbutils method)
(BioSQL.DBUtils.Psycopg2_dbutils method)
B
b() (Bio.Graphics.ColorSpiral.ColorSpiral property)
B() (Bio.Sequencing.Applications.BwaAlignCommandline property)
b() (Bio.Sequencing.Applications.BwaAlignCommandline property)
(Bio.Sequencing.Applications.BwaBwaswCommandline property)
B() (Bio.Sequencing.Applications.BwaMemCommandline property)
b() (Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
B() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
b() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
(Bio.Sequencing.Applications.SamtoolsPhaseCommandline property)
(Bio.Sequencing.Applications.SamtoolsViewCommandline property)
b1() (Bio.Sequencing.Applications.BwaAlignCommandline property)
b2() (Bio.Sequencing.Applications.BwaAlignCommandline property)
back_table (Bio.Data.CodonTable.CodonTable attribute)
back_transcribe() (Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(in module Bio.Seq)
background() (Bio.motifs.Motif property)
backward_algorithm() (Bio.HMM.DynamicProgramming.AbstractDPAlgorithms method)
bam() (Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
bam_file() (Bio.Sequencing.Applications.SamtoolsReheaderCommandline property)
bams() (Bio.Sequencing.Applications.SamtoolsCatCommandline property)
BarChartDistribution (class in Bio.Graphics.Distribution)
BASE_FEATURE_FORMAT (Bio.GenBank.Record.Record attribute)
BASE_FORMAT (Bio.GenBank.Record.Record attribute)
base_id() (Bio.motifs.jaspar.Motif property)
basefreq() (Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
Baseml (class in Bio.Phylo.PAML.baseml)
BasemlError
BaumWelchTrainer (class in Bio.HMM.Trainer)
bc() (Bio.Phylo.PhyloXMLIO.Writer method)
BeforePosition (class in Bio.SeqFeature)
best() (Bio.Emboss.Applications.Est2GenomeCommandline property)
best_hit_overhang() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
best_hit_score_edge() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
BetweenPosition (class in Bio.SeqFeature)
bf_search() (in module Bio.Pathway.Rep.MultiGraph)
bgcolor() (Bio.KEGG.KGML.KGML_pathway.Graphics property)
BgzfBlocks() (in module Bio.bgzf)
BgzfReader (class in Bio.bgzf)
BgzfWriter (class in Bio.bgzf)
binary_characters() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
binary_constraint() (Bio.Phylo.Applications.RaxmlCommandline property)
BinaryCharacters (class in Bio.Phylo.PhyloXML)
Bio
module
Bio.Affy
module
Bio.Affy.CelFile
module
Bio.Align
module
Bio.Align.AlignInfo
module
Bio.Align.Applications
module
Bio.Align.substitution_matrices
module
Bio.AlignIO
module
Bio.AlignIO.ClustalIO
module
Bio.AlignIO.EmbossIO
module
Bio.AlignIO.FastaIO
module
Bio.AlignIO.Interfaces
module
Bio.AlignIO.MafIO
module
Bio.AlignIO.MauveIO
module
Bio.AlignIO.MsfIO
module
Bio.AlignIO.NexusIO
module
Bio.AlignIO.PhylipIO
module
Bio.AlignIO.StockholmIO
module
Bio.Alphabet
module
Bio.Application
module
Bio.bgzf
module
Bio.Blast
module
Bio.Blast.Applications
module
Bio.Blast.NCBIWWW
module
Bio.Blast.NCBIXML
module
Bio.Blast.ParseBlastTable
module
Bio.Blast.Record
module
Bio.CAPS
module
Bio.Cluster
module
Bio.codonalign
module
Bio.codonalign.chisq
module
Bio.codonalign.codonalignment
module
Bio.codonalign.codonseq
module
Bio.Compass
module
Bio.Crystal
module
Bio.Data
module
Bio.Data.CodonTable
module
Bio.Data.IUPACData
module
Bio.Data.SCOPData
module
Bio.Emboss
module
Bio.Emboss.Applications
module
Bio.Emboss.Primer3
module
Bio.Emboss.PrimerSearch
module
Bio.Entrez
module
Bio.Entrez.Parser
module
Bio.ExPASy
module
Bio.ExPASy.cellosaurus
module
Bio.ExPASy.Enzyme
module
Bio.ExPASy.Prodoc
module
Bio.ExPASy.Prosite
module
Bio.ExPASy.ScanProsite
module
Bio.File
module
Bio.FSSP
module
Bio.FSSP.fssp_rec
module
Bio.FSSP.FSSPTools
module
Bio.GenBank
module
Bio.GenBank.Record
module
Bio.GenBank.Scanner
module
Bio.GenBank.utils
module
Bio.Geo
module
Bio.Geo.Record
module
Bio.Graphics
module
Bio.Graphics.BasicChromosome
module
Bio.Graphics.ColorSpiral
module
Bio.Graphics.Comparative
module
Bio.Graphics.DisplayRepresentation
module
Bio.Graphics.Distribution
module
Bio.Graphics.GenomeDiagram
module
Bio.Graphics.KGML_vis
module
Bio.HMM
module
Bio.HMM.DynamicProgramming
module
Bio.HMM.MarkovModel
module
Bio.HMM.Trainer
module
Bio.HMM.Utilities
module
Bio.KEGG
module
Bio.KEGG.Compound
module
Bio.KEGG.Enzyme
module
Bio.KEGG.Gene
module
Bio.KEGG.KGML
module
Bio.KEGG.KGML.KGML_parser
module
Bio.KEGG.KGML.KGML_pathway
module
Bio.KEGG.Map
module
Bio.KEGG.REST
module
Bio.kNN
module
Bio.LogisticRegression
module
Bio.MarkovModel
module
Bio.MaxEntropy
module
Bio.Medline
module
Bio.motifs
module
Bio.motifs.alignace
module
Bio.motifs.applications
module
Bio.motifs.clusterbuster
module
Bio.motifs.jaspar
module
Bio.motifs.jaspar.db
module
Bio.motifs.mast
module
Bio.motifs.matrix
module
Bio.motifs.meme
module
Bio.motifs.minimal
module
Bio.motifs.pfm
module
Bio.motifs.thresholds
module
Bio.motifs.transfac
module
Bio.motifs.xms
module
Bio.NaiveBayes
module
Bio.Nexus
module
Bio.Nexus.Nexus
module
Bio.Nexus.Nodes
module
Bio.Nexus.StandardData
module
Bio.Nexus.Trees
module
Bio.NMR
module
Bio.NMR.NOEtools
module
Bio.NMR.xpktools
module
Bio.pairwise2
module
Bio.Pathway
module
Bio.Pathway.Rep
module
Bio.Pathway.Rep.Graph
module
Bio.Pathway.Rep.MultiGraph
module
Bio.PDB
module
Bio.PDB.AbstractPropertyMap
module
Bio.PDB.Atom
module
Bio.PDB.Chain
module
Bio.PDB.Dice
module
Bio.PDB.DSSP
module
Bio.PDB.Entity
module
Bio.PDB.FragmentMapper
module
Bio.PDB.HSExposure
module
Bio.PDB.ic_data
module
Bio.PDB.ic_rebuild
module
Bio.PDB.internal_coords
module
Bio.PDB.MMCIF2Dict
module
Bio.PDB.mmcifio
module
Bio.PDB.MMCIFParser
module
Bio.PDB.mmtf
module
Bio.PDB.mmtf.DefaultParser
module
Bio.PDB.mmtf.mmtfio
module
Bio.PDB.Model
module
Bio.PDB.NACCESS
module
Bio.PDB.NeighborSearch
module
Bio.PDB.parse_pdb_header
module
Bio.PDB.PDBExceptions
module
Bio.PDB.PDBIO
module
Bio.PDB.PDBList
module
Bio.PDB.PDBParser
module
Bio.PDB.PICIO
module
Bio.PDB.Polypeptide
module
Bio.PDB.PSEA
module
Bio.PDB.QCPSuperimposer
module
Bio.PDB.Residue
module
Bio.PDB.ResidueDepth
module
Bio.PDB.SCADIO
module
Bio.PDB.Selection
module
Bio.PDB.Structure
module
Bio.PDB.StructureAlignment
module
Bio.PDB.StructureBuilder
module
Bio.PDB.Superimposer
module
Bio.PDB.vectors
module
Bio.phenotype
module
Bio.phenotype.phen_micro
module
Bio.phenotype.pm_fitting
module
Bio.Phylo
module
Bio.Phylo.Applications
module
Bio.Phylo.BaseTree
module
Bio.Phylo.CDAO
module
Bio.Phylo.CDAOIO
module
Bio.Phylo.Consensus
module
Bio.Phylo.Newick
module
Bio.Phylo.NewickIO
module
Bio.Phylo.NeXML
module
Bio.Phylo.NeXMLIO
module
Bio.Phylo.NexusIO
module
Bio.Phylo.PAML
module
Bio.Phylo.PAML.baseml
module
Bio.Phylo.PAML.chi2
module
Bio.Phylo.PAML.codeml
module
Bio.Phylo.PAML.yn00
module
Bio.Phylo.PhyloXML
module
Bio.Phylo.PhyloXMLIO
module
Bio.Phylo.TreeConstruction
module
Bio.PopGen
module
Bio.PopGen.GenePop
module
Bio.PopGen.GenePop.Controller
module
Bio.PopGen.GenePop.EasyController
module
Bio.PopGen.GenePop.FileParser
module
Bio.PopGen.GenePop.LargeFileParser
module
Bio.Restriction
module
Bio.Restriction.PrintFormat
module
Bio.Restriction.Restriction
module
Bio.Restriction.Restriction_Dictionary
module
Bio.SCOP
module
Bio.SCOP.Cla
module
Bio.SCOP.Des
module
Bio.SCOP.Dom
module
Bio.SCOP.Hie
module
Bio.SCOP.Raf
module
Bio.SCOP.Residues
module
Bio.SearchIO
module
Bio.SearchIO.BlastIO
module
Bio.SearchIO.BlastIO.blast_tab
module
Bio.SearchIO.BlastIO.blast_text
module
Bio.SearchIO.BlastIO.blast_xml
module
Bio.SearchIO.BlatIO
module
Bio.SearchIO.ExonerateIO
module
Bio.SearchIO.ExonerateIO.exonerate_cigar
module
Bio.SearchIO.ExonerateIO.exonerate_text
module
Bio.SearchIO.ExonerateIO.exonerate_vulgar
module
Bio.SearchIO.FastaIO
module
Bio.SearchIO.HHsuiteIO
module
Bio.SearchIO.HHsuiteIO.hhsuite2_text
module
Bio.SearchIO.HmmerIO
module
Bio.SearchIO.HmmerIO.hmmer2_text
module
Bio.SearchIO.HmmerIO.hmmer3_domtab
module
Bio.SearchIO.HmmerIO.hmmer3_tab
module
Bio.SearchIO.HmmerIO.hmmer3_text
module
Bio.SearchIO.InterproscanIO
module
Bio.SearchIO.InterproscanIO.interproscan_xml
module
Bio.Seq
module
Bio.SeqFeature
module
Bio.SeqIO
module
Bio.SeqIO.AbiIO
module
Bio.SeqIO.AceIO
module
Bio.SeqIO.FastaIO
module
Bio.SeqIO.GckIO
module
Bio.SeqIO.IgIO
module
Bio.SeqIO.InsdcIO
module
Bio.SeqIO.Interfaces
module
Bio.SeqIO.NibIO
module
Bio.SeqIO.PdbIO
module
Bio.SeqIO.PhdIO
module
Bio.SeqIO.PirIO
module
Bio.SeqIO.QualityIO
module
Bio.SeqIO.SeqXmlIO
module
Bio.SeqIO.SffIO
module
Bio.SeqIO.SnapGeneIO
module
Bio.SeqIO.SwissIO
module
Bio.SeqIO.TabIO
module
Bio.SeqIO.UniprotIO
module
Bio.SeqIO.XdnaIO
module
Bio.SeqRecord
module
Bio.Sequencing
module
Bio.Sequencing.Ace
module
Bio.Sequencing.Applications
module
Bio.Sequencing.Phd
module
Bio.SeqUtils
module
Bio.SeqUtils.CheckSum
module
Bio.SeqUtils.CodonUsage
module
Bio.SeqUtils.CodonUsageIndices
module
Bio.SeqUtils.IsoelectricPoint
module
Bio.SeqUtils.lcc
module
Bio.SeqUtils.MeltingTemp
module
Bio.SeqUtils.ProtParam
module
Bio.SeqUtils.ProtParamData
module
Bio.Statistics
module
Bio.Statistics.lowess
module
Bio.SubsMat
module
Bio.SubsMat.FreqTable
module
Bio.SubsMat.MatrixInfo
module
Bio.SVDSuperimposer
module
Bio.SwissProt
module
Bio.SwissProt.KeyWList
module
Bio.TogoWS
module
Bio.UniGene
module
Bio.UniProt
module
Bio.UniProt.GOA
module
Bio.Wise
module
Bio.Wise.dnal
module
Bio.Wise.psw
module
bionj() (Bio.Phylo.Applications.FastTreeCommandline property)
BiopythonDeprecationWarning
BiopythonExperimentalWarning
BiopythonParserWarning
BiopythonWarning
BioSeqDatabase (class in BioSQL.BioSeqDatabase)
BioSQL
module
BioSQL.BioSeq
module
BioSQL.BioSeqDatabase
module
BioSQL.DBUtils
module
BioSQL.Loader
module
bipartition_filename() (Bio.Phylo.Applications.RaxmlCommandline property)
bl() (Bio.Align.Applications.MafftCommandline property)
Blast (class in Bio.Blast.Record)
BlastParser (class in Bio.Blast.NCBIXML)
BlastTabIndexer (class in Bio.SearchIO.BlastIO.blast_tab)
BlastTableEntry (class in Bio.Blast.ParseBlastTable)
BlastTableReader (class in Bio.Blast.ParseBlastTable)
BlastTableRec (class in Bio.Blast.ParseBlastTable)
BlastTabParser (class in Bio.SearchIO.BlastIO.blast_tab)
BlastTabWriter (class in Bio.SearchIO.BlastIO.blast_tab)
BlastTextParser (class in Bio.SearchIO.BlastIO.blast_text)
BlastXmlIndexer (class in Bio.SearchIO.BlastIO.blast_xml)
BlastXmlParser (class in Bio.SearchIO.BlastIO.blast_xml)
BlastXmlWriter (class in Bio.SearchIO.BlastIO.blast_xml)
BlatPslIndexer (class in Bio.SearchIO.BlatIO)
BlatPslParser (class in Bio.SearchIO.BlatIO)
BlatPslWriter (class in Bio.SearchIO.BlatIO)
BLOCK (Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute)
Block (class in Bio.Nexus.Nexus)
block_size (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute)
BLOCKS_PER_LINE (Bio.SeqIO.InsdcIO.EmblWriter attribute)
blocksize() (Bio.Emboss.Applications.FSeqBootCommandline property)
blue() (Bio.Phylo.PhyloXMLIO.Writer method)
boot() (Bio.Phylo.Applications.FastTreeCommandline property)
bootlabels() (Bio.Align.Applications.ClustalwCommandline property)
bootstrap() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Nexus.Nexus.Nexus method)
(Bio.Phylo.Applications.PhymlCommandline property)
(in module Bio.Phylo.Consensus)
bootstrap_branch_lengths() (Bio.Phylo.Applications.RaxmlCommandline property)
bootstrap_consensus() (in module Bio.Phylo.Consensus)
bootstrap_seed() (Bio.Phylo.Applications.RaxmlCommandline property)
bootstrap_trees() (in module Bio.Phylo.Consensus)
bounds() (Bio.KEGG.KGML.KGML_pathway.Entry property)
(Bio.KEGG.KGML.KGML_pathway.Graphics property)
(Bio.KEGG.KGML.KGML_pathway.Pathway property)
boutfeat() (Bio.Emboss.Applications.DiffseqCommandline property)
branch_length() (Bio.Phylo.PhyloXMLIO.Writer method)
BranchColor (class in Bio.Phylo.BaseTree)
(class in Bio.Phylo.PhyloXML)
branchlength2support() (Bio.Nexus.Trees.Tree method)
brenner() (Bio.Align.Applications.MuscleCommandline property)
brief() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
bs (class in Bio.Sequencing.Ace)
bsequence() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
build() (in module Bio.codonalign)
build_glyCB() (Bio.PDB.internal_coords.IC_Residue method)
build_rak_cache() (Bio.PDB.internal_coords.IC_Residue method)
build_resnum_list() (Bio.FSSP.FSSPAlignDict method)
build_tree() (Bio.Phylo.TreeConstruction.DistanceTreeConstructor method)
(Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor method)
(Bio.Phylo.TreeConstruction.TreeConstructor method)
BwaAlignCommandline (class in Bio.Sequencing.Applications)
BwaBwaswCommandline (class in Bio.Sequencing.Applications)
BwaIndexCommandline (class in Bio.Sequencing.Applications)
BwaMemCommandline (class in Bio.Sequencing.Applications)
BwaSampeCommandline (class in Bio.Sequencing.Applications)
BwaSamseCommandline (class in Bio.Sequencing.Applications)
C
c() (Bio.Sequencing.Applications.BwaAlignCommandline property)
(Bio.Sequencing.Applications.BwaBwaswCommandline property)
(Bio.Sequencing.Applications.BwaIndexCommandline property)
C() (Bio.Sequencing.Applications.BwaMemCommandline property)
c() (Bio.Sequencing.Applications.BwaMemCommandline property)
C() (Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
c() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
ca_depth() (in module Bio.PDB.ResidueDepth)
cai_for_gene() (Bio.SeqUtils.CodonUsage.CodonAdaptationIndex method)
cal_dn_ds() (in module Bio.codonalign.codonseq)
calc_affine_penalty() (in module Bio.pairwise2)
calc_allele_genotype_freqs() (Bio.PopGen.GenePop.Controller.GenePopController method)
calc_angle() (in module Bio.PDB.vectors)
calc_dihedral() (in module Bio.PDB.vectors)
calc_diversities_fis_with_identity() (Bio.PopGen.GenePop.Controller.GenePopController method)
calc_diversities_fis_with_size() (Bio.PopGen.GenePop.Controller.GenePopController method)
calc_fst_all() (Bio.PopGen.GenePop.Controller.GenePopController method)
calc_fst_pair() (Bio.PopGen.GenePop.Controller.GenePopController method)
calc_ibd() (Bio.PopGen.GenePop.EasyController.EasyController method)
calc_ibd_diplo() (Bio.PopGen.GenePop.Controller.GenePopController method)
calc_ibd_haplo() (Bio.PopGen.GenePop.Controller.GenePopController method)
calc_rho_all() (Bio.PopGen.GenePop.Controller.GenePopController method)
calc_rho_pair() (Bio.PopGen.GenePop.Controller.GenePopController method)
calculate() (Bio.motifs.matrix.PositionSpecificScoringMatrix method)
(in module Bio.kNN)
(in module Bio.LogisticRegression)
(in module Bio.MaxEntropy)
(in module Bio.NaiveBayes)
calculate_pseudocounts() (in module Bio.motifs.jaspar)
calculate_relative_entropy() (Bio.SubsMat.LogOddsMatrix method)
(Bio.SubsMat.SubstitutionMatrix method)
CaPPBuilder (class in Bio.PDB.Polypeptide)
CAPSMap (class in Bio.CAPS)
carboxyl() (Bio.Emboss.Applications.IepCommandline property)
case() (Bio.Align.Applications.ClustalwCommandline property)
cat() (Bio.Phylo.Applications.FastTreeCommandline property)
categories() (Bio.Emboss.Applications.FDNADistCommandline property)
catergories() (Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
cdao_to_obo() (in module Bio.Phylo.NeXMLIO)
cdf_chi2() (in module Bio.Phylo.PAML.chi2)
center() (Bio.Align.Applications.MuscleCommandline property)
centre() (Bio.KEGG.KGML.KGML_pathway.Graphics property)
Chain (class in Bio.Crystal)
(class in Bio.Nexus.Nodes)
(class in Bio.PDB.Chain)
chain_id (Bio.FSSP.fssp_rec.align attribute)
ChainException
ChainSelector (class in Bio.PDB.Dice)
characterDataHandlerEscape() (Bio.Entrez.Parser.DataHandler method)
characterDataHandlerRaw() (Bio.Entrez.Parser.DataHandler method)
characters() (Bio.ExPASy.ScanProsite.ContentHandler method)
(Bio.SeqIO.SeqXmlIO.ContentHandler method)
CharBuffer (class in Bio.Nexus.Nexus)
charge_at_pH() (Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint method)
(Bio.SeqUtils.ProtParam.ProteinAnalysis method)
check() (Bio.Align.Applications.ClustalwCommandline property)
checkpoints() (Bio.Phylo.Applications.RaxmlCommandline property)
chem_correction() (in module Bio.SeqUtils.MeltingTemp)
child_edges() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
children() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
chisqprob() (in module Bio.codonalign.chisq)
Chromosome (class in Bio.Graphics.BasicChromosome)
ChromosomeCounts (class in Bio.Graphics.DisplayRepresentation)
ChromosomeSegment (class in Bio.Graphics.BasicChromosome)
CifAtomIterator() (in module Bio.SeqIO.PdbIO)
CifSeqresIterator() (in module Bio.SeqIO.PdbIO)
Clade (class in Bio.Phylo.BaseTree)
(class in Bio.Phylo.CDAO)
(class in Bio.Phylo.Newick)
(class in Bio.Phylo.NeXML)
(class in Bio.Phylo.PhyloXML)
clade() (Bio.Phylo.BaseTree.Tree property)
(Bio.Phylo.PhyloXMLIO.Writer method)
clade_relation() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
CladeRelation (class in Bio.Phylo.PhyloXML)
classify() (in module Bio.kNN)
(in module Bio.LogisticRegression)
(in module Bio.MaxEntropy)
(in module Bio.NaiveBayes)
clean() (Bio.AlignIO.Interfaces.AlignmentWriter method)
(Bio.SeqIO.Interfaces.SequenceWriter method)
clean_value() (Bio.GenBank.utils.FeatureValueCleaner method)
clear() (Bio.Crystal.Crystal method)
clear_ic() (Bio.PDB.internal_coords.IC_Chain method)
clear_transforms() (Bio.PDB.internal_coords.IC_Residue method)
close() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
(Bio.Phylo.Applications.FastTreeCommandline property)
(BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.DBServer method)
ClustalIterator (class in Bio.AlignIO.ClustalIO)
ClustalOmegaCommandline (class in Bio.Align.Applications)
clustalout() (Bio.Align.Applications.MafftCommandline property)
clustalw() (Bio.Align.Applications.MSAProbsCommandline property)
(Bio.Align.Applications.ProbconsCommandline property)
ClustalwCommandline (class in Bio.Align.Applications)
ClustalWriter (class in Bio.AlignIO.ClustalIO)
cluster() (Bio.Align.Applications.MuscleCommandline property)
cluster1() (Bio.Align.Applications.MuscleCommandline property)
cluster2() (Bio.Align.Applications.MuscleCommandline property)
cluster_threshold() (Bio.Phylo.Applications.RaxmlCommandline property)
cluster_threshold_fast() (Bio.Phylo.Applications.RaxmlCommandline property)
clustercentroids() (Bio.Cluster.Record method)
(in module Bio.Cluster)
clusterdistance() (Bio.Cluster.Record method)
(in module Bio.Cluster)
clustering() (Bio.Align.Applications.ClustalwCommandline property)
clusteringout() (Bio.Align.Applications.ClustalOmegaCommandline property)
clustersize() (Bio.Align.Applications.ClustalOmegaCommandline property)
clw() (Bio.Align.Applications.MuscleCommandline property)
clwout() (Bio.Align.Applications.MuscleCommandline property)
clwstrict() (Bio.Align.Applications.MuscleCommandline property)
clwstrictout() (Bio.Align.Applications.MuscleCommandline property)
Cmodulo (Bio.Restriction.PrintFormat.PrintFormat attribute)
cmp_sccs() (in module Bio.SCOP)
code() (Bio.Phylo.PhyloXMLIO.Writer method)
Codeml (class in Bio.Phylo.PAML.codeml)
CodemlError
codon() (Bio.Align.Applications.PrankCommandline property)
CodonAdaptationIndex (class in Bio.SeqUtils.CodonUsage)
CodonAlignment (class in Bio.codonalign.codonalignment)
CodonSeq (class in Bio.codonalign.codonseq)
CodonTable (class in Bio.Data.CodonTable)
collapse() (Bio.Nexus.Nodes.Chain method)
(Bio.Phylo.BaseTree.TreeMixin method)
collapse_all() (Bio.Phylo.BaseTree.TreeMixin method)
collapse_genera() (Bio.Nexus.Trees.Tree method)
color() (Bio.Phylo.BaseTree.Clade property)
(Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
color_names (Bio.Phylo.BaseTree.BranchColor attribute)
color_to_reportlab() (in module Bio.Graphics.KGML_vis)
ColorSpiral (class in Bio.Graphics.ColorSpiral)
ColorTranslator (class in Bio.Graphics.GenomeDiagram)
column_annotations() (Bio.Align.MultipleSeqAlignment property)
ColumnUnit (class in Bio.Wise.psw)
combine() (in module Bio.Nexus.Nexus)
Commandline (class in Bio.Nexus.Nexus)
commit() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.DBServer method)
common_ancestor() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
common_name() (Bio.Phylo.PhyloXMLIO.Writer method)
comp_based_stats() (Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
ComparativeScatterPlot (class in Bio.Graphics.Comparative)
compare_residues() (in module Bio.PDB.ic_rebuild)
complement() (Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(in module Bio.Seq)
complement_rna() (Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(in module Bio.Seq)
Component (class in Bio.KEGG.KGML.KGML_pathway)
CompoundLocation (class in Bio.SeqFeature)
compounds() (Bio.KEGG.KGML.KGML_pathway.Pathway property)
Confidence (class in Bio.Phylo.PhyloXML)
confidence() (Bio.Phylo.PhyloXML.Clade property)
(Bio.Phylo.PhyloXML.Phylogeny property)
(Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
consensus() (Bio.motifs.matrix.GenericPositionMatrix property)
(Bio.motifs.Motif property)
(in module Bio.Nexus.Trees)
consistency() (Bio.Align.Applications.MSAProbsCommandline property)
(Bio.Align.Applications.ProbconsCommandline property)
ConsoleWidth (Bio.Restriction.PrintFormat.PrintFormat attribute)
constant() (Bio.Nexus.Nexus.Nexus method)
constraints() (Bio.Phylo.Applications.FastTreeCommandline property)
constraintWeight() (Bio.Phylo.Applications.FastTreeCommandline property)
ContentHandler (class in Bio.ExPASy.ScanProsite)
(class in Bio.SeqIO.SeqXmlIO)
Contig (class in Bio.Sequencing.Ace)
convert() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.PrankCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
(in module Bio.AlignIO)
(in module Bio.SearchIO)
(in module Bio.SeqIO)
(in module Bio.TogoWS)
convert_absolute_support() (Bio.Nexus.Trees.Tree method)
coord_space() (in module Bio.PDB.vectors)
coords() (Bio.KEGG.KGML.KGML_pathway.Graphics property)
coords_to_residue() (Bio.PDB.internal_coords.IC_Residue method)
coords_to_structure() (Bio.PDB.internal_coords.IC_Chain method)
copy() (Bio.Align.substitution_matrices.Array method)
(Bio.Crystal.Crystal method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.vectors.Vector method)
core() (Bio.Align.Applications.MuscleCommandline property)
cores() (Bio.Sequencing.Applications.NovoalignCommandline property)
CorruptedXMLError
count() (Bio.Crystal.Chain method)
(Bio.motifs.Instances method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
count_amino_acids() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
count_overlap() (Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
count_terminals() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
crc32() (in module Bio.SeqUtils.CheckSum)
crc64() (in module Bio.SeqUtils.CheckSum)
create() (in module Bio.motifs)
create_contingency_tables() (Bio.PopGen.GenePop.Controller.GenePopController method)
crop_matrix() (Bio.Nexus.Nexus.Nexus method)
CrossLink (class in Bio.Graphics.GenomeDiagram)
Crystal (class in Bio.Crystal)
CrystalError
cs() (Bio.Align.Applications.DialignCommandline property)
cstatus() (Bio.Nexus.Nexus.Nexus method)
CsvIterator() (in module Bio.phenotype.phen_micro)
ct (class in Bio.Sequencing.Ace)
culling_limit() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
cut() (Bio.Cluster.Tree method)
cw() (Bio.Align.Applications.DialignCommandline property)
D
d() (Bio.Align.Applications.PrankCommandline property)
(Bio.Sequencing.Applications.BwaAlignCommandline property)
(Bio.Sequencing.Applications.BwaMemCommandline property)
D() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
d() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
d2h (Bio.PDB.internal_coords.AtomKey attribute)
darken() (in module Bio.Graphics.KGML_vis)
data() (BioSQL.BioSeq.DBSeq property)
data_generator() (Bio.PopGen.GenePop.LargeFileParser.Record method)
data_quartiles() (Bio.Graphics.GenomeDiagram.GraphSet method)
data_table() (in module Bio.NMR.xpktools)
database() (Bio.Sequencing.Applications.NovoalignCommandline property)
DatabaseLoader (class in BioSQL.Loader)
DatabaseRemover (class in BioSQL.Loader)
DatabaseReport (class in Bio.Blast.Record)
datafile() (Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
DataHandler (class in Bio.Entrez.Parser)
datatype() (Bio.Phylo.Applications.PhymlCommandline property)
Date (class in Bio.Phylo.PhyloXML)
date() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
db() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
db_gencode() (Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
db_hard_mask() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
db_soft_mask() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
DBSeq (class in BioSQL.BioSeq)
DBSeqRecord (class in BioSQL.BioSeq)
DBServer (class in BioSQL.BioSeqDatabase)
dbsize() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
dbtype() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
dbxrefs() (BioSQL.BioSeq.DBSeqRecord property)
dealign() (Bio.Align.Applications.ClustalOmegaCommandline property)
debug() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
DEFAULT_PSEUDO (Bio.HMM.MarkovModel.MarkovModelBuilder attribute)
default_startpos() (Bio.PDB.internal_coords.IC_Residue method)
degenerate_consensus() (Bio.motifs.matrix.GenericPositionMatrix property)
(Bio.motifs.Motif property)
del_feature() (Bio.Graphics.GenomeDiagram.FeatureSet method)
del_graph() (Bio.Graphics.GenomeDiagram.GraphSet method)
del_set() (Bio.Graphics.GenomeDiagram.Track method)
del_track() (Bio.Graphics.GenomeDiagram.Diagram method)
depths() (Bio.Phylo.BaseTree.TreeMixin method)
desc() (Bio.Phylo.PhyloXMLIO.Writer method)
Description (class in Bio.Blast.Record)
description() (Bio.Phylo.PhyloXMLIO.Writer method)
DescriptionExt (class in Bio.Blast.Record)
DescriptionExtItem (class in Bio.Blast.Record)
destroy_transition() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
detach_child() (Bio.PDB.Entity.Entity method)
detach_parent() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
df_search() (in module Bio.Pathway.Rep.MultiGraph)
diagbreak() (Bio.Align.Applications.MuscleCommandline property)
diaglength() (Bio.Align.Applications.MuscleCommandline property)
diagmargin() (Bio.Align.Applications.MuscleCommandline property)
Diagram (class in Bio.Graphics.GenomeDiagram)
diags() (Bio.Align.Applications.MuscleCommandline property)
DialignCommandline (class in Bio.Align.Applications)
dictionary_match (class in Bio.pairwise2)
DictionaryElement (class in Bio.Entrez.Parser)
die() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
DifferentialCutsite (class in Bio.CAPS)
DiffseqCommandline (class in Bio.Emboss.Applications)
Dihedron (class in Bio.PDB.internal_coords)
dimer() (Bio.Align.Applications.MuscleCommandline property)
directory() (Bio.Entrez.Parser.DataHandler property)
disordered_add() (Bio.PDB.Atom.DisorderedAtom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Residue.DisorderedResidue method)
disordered_get() (Bio.PDB.Entity.DisorderedEntityWrapper method)
disordered_get_id_list() (Bio.PDB.Entity.DisorderedEntityWrapper method)
disordered_get_list() (Bio.PDB.Atom.DisorderedAtom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
disordered_has_id() (Bio.PDB.Entity.DisorderedEntityWrapper method)
disordered_select() (Bio.PDB.Entity.DisorderedEntityWrapper method)
DisorderedAtom (class in Bio.PDB.Atom)
DisorderedEntityWrapper (class in Bio.PDB.Entity)
DisorderedResidue (class in Bio.PDB.Residue)
display() (Bio.Nexus.Trees.Tree method)
dist_pearson() (Bio.motifs.matrix.PositionSpecificScoringMatrix method)
dist_pearson_at() (Bio.motifs.matrix.PositionSpecificScoringMatrix method)
distance() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
distance1() (Bio.Align.Applications.MuscleCommandline property)
distance2() (Bio.Align.Applications.MuscleCommandline property)
DistanceCalculator (class in Bio.Phylo.TreeConstruction)
DistanceMatrix (class in Bio.Phylo.TreeConstruction)
distancematrix() (Bio.Cluster.Record method)
(in module Bio.Cluster)
DistanceTreeConstructor (class in Bio.Phylo.TreeConstruction)
distmat_full() (Bio.Align.Applications.ClustalOmegaCommandline property)
distmat_full_iter() (Bio.Align.Applications.ClustalOmegaCommandline property)
distmat_in() (Bio.Align.Applications.ClustalOmegaCommandline property)
distmat_out() (Bio.Align.Applications.ClustalOmegaCommandline property)
Distribution (class in Bio.Phylo.PhyloXML)
distribution() (Bio.motifs.matrix.PositionSpecificScoringMatrix method)
(Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
DistributionPage (class in Bio.Graphics.Distribution)
disulphides() (Bio.Emboss.Applications.IepCommandline property)
dna_models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute)
dnaconc() (Bio.Emboss.Applications.Primer3Commandline property)
dnafreqs() (Bio.Align.Applications.PrankCommandline property)
dnamatrix() (Bio.Align.Applications.ClustalwCommandline property)
Domain (class in Bio.SCOP)
domain() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
domain_architecture() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
domain_inclusion_ethresh() (Bio.Blast.Applications.NcbideltablastCommandline property)
DomainArchitecture (class in Bio.Phylo.PhyloXML)
domainsClusteredByEv() (Bio.SCOP.Astral method)
domainsClusteredById() (Bio.SCOP.Astral method)
dotdiff() (Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
dots() (Bio.Align.Applications.PrankCommandline property)
download_entire_pdb() (Bio.PDB.PDBList.PDBList method)
download_obsolete_entries() (Bio.PDB.PDBList.PDBList method)
download_pdb_files() (Bio.PDB.PDBList.PDBList method)
dpparttree() (Bio.Align.Applications.MafftCommandline property)
draw() (Bio.Graphics.BasicChromosome.Chromosome method)
(Bio.Graphics.BasicChromosome.ChromosomeSegment method)
(Bio.Graphics.BasicChromosome.Organism method)
(Bio.Graphics.BasicChromosome.SpacerSegment method)
(Bio.Graphics.Distribution.BarChartDistribution method)
(Bio.Graphics.Distribution.DistributionPage method)
(Bio.Graphics.Distribution.LineDistribution method)
(Bio.Graphics.GenomeDiagram.Diagram method)
(Bio.Graphics.KGML_vis.KGMLCanvas method)
draw_to_file() (Bio.Graphics.Comparative.ComparativeScatterPlot method)
ds (class in Bio.Sequencing.Ace)
ds() (Bio.Align.Applications.DialignCommandline property)
DSSP (class in Bio.PDB.DSSP)
dssp_dict_from_pdb_file() (in module Bio.PDB.DSSP)
dtype() (Bio.Emboss.Applications.FTreeDistCommandline property)
dumb_consensus() (Bio.Align.AlignInfo.SummaryInfo method)
duplications() (Bio.Phylo.PhyloXMLIO.Writer method)
dust() (Bio.Blast.Applications.NcbiblastnCommandline property)
E
E() (Bio.Sequencing.Applications.BwaAlignCommandline property)
e() (Bio.Sequencing.Applications.BwaAlignCommandline property)
E() (Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
e() (Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
E() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
e() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
ease() (Bio.Emboss.Applications.FProtDistCommandline property)
EasyController (class in Bio.PopGen.GenePop.EasyController)
ecitmatch() (in module Bio.Entrez)
edges() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
Edron (class in Bio.PDB.internal_coords)
edron_re (Bio.PDB.internal_coords.Edron attribute)
efetch() (in module Bio.Entrez)
egquery() (in module Bio.Entrez)
einfo() (in module Bio.Entrez)
EInvertedCommandline (class in Bio.Emboss.Applications)
element() (Bio.KEGG.KGML.KGML_pathway.Component property)
(Bio.KEGG.KGML.KGML_pathway.Entry property)
(Bio.KEGG.KGML.KGML_pathway.Graphics property)
(Bio.KEGG.KGML.KGML_pathway.Pathway property)
(Bio.KEGG.KGML.KGML_pathway.Reaction property)
(Bio.KEGG.KGML.KGML_pathway.Relation property)
elementDecl() (Bio.Entrez.Parser.DataHandler method)
elink() (in module Bio.Entrez)
em0() (Bio.Sequencing.Applications.SamtoolsTargetcutCommandline property)
em1() (Bio.Sequencing.Applications.SamtoolsTargetcutCommandline property)
em2() (Bio.Sequencing.Applications.SamtoolsTargetcutCommandline property)
EMBL_INDENT (Bio.GenBank.Scanner.EmblScanner attribute)
EMBL_SPACER (Bio.GenBank.Scanner.EmblScanner attribute)
EmblCdsFeatureIterator (class in Bio.SeqIO.InsdcIO)
EmblIterator (class in Bio.SeqIO.InsdcIO)
EmblScanner (class in Bio.GenBank.Scanner)
EmblWriter (class in Bio.SeqIO.InsdcIO)
EmbossIterator (class in Bio.AlignIO.EmbossIO)
emissions() (Bio.Align.Applications.ProbconsCommandline property)
encode() (Bio.Seq.Seq method)
end() (Bio.SeqFeature.CompoundLocation property)
(Bio.SeqFeature.FeatureLocation property)
endA() (Bio.Graphics.GenomeDiagram.CrossLink property)
endB() (Bio.Graphics.GenomeDiagram.CrossLink property)
endDBRefElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
endDescriptionElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
endElement() (Bio.ExPASy.ScanProsite.ContentHandler method)
endElementHandler() (Bio.Entrez.Parser.DataHandler method)
endEntryElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
endErrorElementHandler() (Bio.Entrez.Parser.DataHandler method)
endextend() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
endgaps() (Bio.Align.Applications.ClustalwCommandline property)
endIntegerElementHandler() (Bio.Entrez.Parser.DataHandler method)
endNamespaceDeclHandler() (Bio.Entrez.Parser.DataHandler method)
endnum_re (Bio.PDB.internal_coords.AtomKey attribute)
endopen() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
endPropertyElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
endRawElementHandler() (Bio.Entrez.Parser.DataHandler method)
endSequenceElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
endSeqXMLElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
endSkipElementHandler() (Bio.Entrez.Parser.DataHandler method)
endSpeciesElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
endStringElementHandler() (Bio.Entrez.Parser.DataHandler method)
endswith() (Bio.Seq.Seq method)
endweight() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
Entity (class in Bio.PDB.Entity)
entrez_query() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
Entry (class in Bio.KEGG.KGML.KGML_pathway)
entry() (Bio.KEGG.KGML.KGML_pathway.Reaction property)
(in module Bio.TogoWS)
entry1() (Bio.KEGG.KGML.KGML_pathway.Relation property)
entry2() (Bio.KEGG.KGML.KGML_pathway.Relation property)
enumerate_atoms() (in module Bio.PDB.PICIO)
ep() (Bio.Align.Applications.MafftCommandline property)
epost() (in module Bio.Entrez)
epsilon() (Bio.Phylo.Applications.RaxmlCommandline property)
equal_weight() (in module Bio.kNN)
error() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
errorfile() (Bio.Emboss.Applications.NeedleallCommandline property)
esearch() (in module Bio.Entrez)
espell() (in module Bio.Entrez)
est() (Bio.Emboss.Applications.Est2GenomeCommandline property)
Est2GenomeCommandline (class in Bio.Emboss.Applications)
estimate_nm() (Bio.PopGen.GenePop.Controller.GenePopController method)
(Bio.PopGen.GenePop.EasyController.EasyController method)
estimate_params() (Bio.HMM.Trainer.AbstractTrainer method)
esummary() (in module Bio.Entrez)
ETandemCommandline (class in Bio.Emboss.Applications)
evalue() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
Events (class in Bio.Phylo.PhyloXML)
events() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
ExactPosition (class in Bio.SeqFeature)
exclude_filename() (Bio.Phylo.Applications.RaxmlCommandline property)
excludedregion() (Bio.Emboss.Applications.Primer3Commandline property)
execute() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.DBUtils.Generic_dbutils method)
(BioSQL.DBUtils.Sqlite_dbutils method)
execute_and_fetch_col0() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.MysqlConnectorAdaptor method)
execute_and_fetchall() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.MysqlConnectorAdaptor method)
execute_one() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.MysqlConnectorAdaptor method)
executemany() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.DBUtils.Generic_dbutils method)
(BioSQL.DBUtils.Sqlite_dbutils method)
ExonerateCigarIndexer (class in Bio.SearchIO.ExonerateIO.exonerate_cigar)
ExonerateCigarParser (class in Bio.SearchIO.ExonerateIO.exonerate_cigar)
ExonerateTextIndexer (class in Bio.SearchIO.ExonerateIO.exonerate_text)
ExonerateTextParser (class in Bio.SearchIO.ExonerateIO.exonerate_text)
ExonerateVulgarIndexer (class in Bio.SearchIO.ExonerateIO.exonerate_vulgar)
ExonerateVulgarParser (class in Bio.SearchIO.ExonerateIO.exonerate_vulgar)
expert() (Bio.Phylo.Applications.FastTreeCommandline property)
explainflag() (Bio.Emboss.Applications.Primer3Commandline property)
export_fasta() (Bio.Nexus.Nexus.Nexus method)
export_phylip() (Bio.Nexus.Nexus.Nexus method)
export_search_strategy() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
ExposureCN (class in Bio.PDB.HSExposure)
extend() (Bio.Align.MultipleSeqAlignment method)
(Bio.SCOP.Raf.SeqMap method)
(Bio.Seq.MutableSeq method)
extension() (Bio.SeqFeature.AfterPosition property)
(Bio.SeqFeature.BeforePosition property)
(Bio.SeqFeature.BetweenPosition property)
(Bio.SeqFeature.ExactPosition property)
(Bio.SeqFeature.OneOfPosition property)
(Bio.SeqFeature.UnknownPosition property)
(Bio.SeqFeature.WithinPosition property)
externalEntityRefHandler() (Bio.Entrez.Parser.DataHandler method)
extract() (Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.FeatureLocation method)
(Bio.SeqFeature.SeqFeature method)
(in module Bio.PDB.Dice)
F
F() (Bio.Align.Applications.PrankCommandline property)
f() (Bio.Align.Applications.PrankCommandline property)
(Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
F() (Bio.Sequencing.Applications.SamtoolsPhaseCommandline property)
f() (Bio.Sequencing.Applications.SamtoolsTargetcutCommandline property)
F() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
f() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
fa() (Bio.Align.Applications.DialignCommandline property)
fast_bam() (Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
(Bio.Sequencing.Applications.SamtoolsViewCommandline property)
fasta() (Bio.Align.Applications.MuscleCommandline property)
fasta_mult_align() (Bio.FSSP.FSSPAlignDict method)
FastaIterator (class in Bio.SeqIO.FastaIO)
FastaM10Indexer (class in Bio.SearchIO.FastaIO)
FastaM10Iterator() (in module Bio.AlignIO.FastaIO)
FastaM10Parser (class in Bio.SearchIO.FastaIO)
fastaout() (Bio.Align.Applications.MuscleCommandline property)
fastapair() (Bio.Align.Applications.MafftCommandline property)
fastaparttree() (Bio.Align.Applications.MafftCommandline property)
FastaTwoLineIterator (class in Bio.SeqIO.FastaIO)
FastaTwoLineParser() (in module Bio.SeqIO.FastaIO)
FastaTwoLineWriter (class in Bio.SeqIO.FastaIO)
FastaWriter (class in Bio.SeqIO.FastaIO)
fastest() (Bio.Phylo.Applications.FastTreeCommandline property)
FastMMCIFParser (class in Bio.PDB.MMCIFParser)
FastqGeneralIterator() (in module Bio.SeqIO.QualityIO)
FastqIlluminaIterator() (in module Bio.SeqIO.QualityIO)
FastqIlluminaWriter (class in Bio.SeqIO.QualityIO)
FastqPhredIterator (class in Bio.SeqIO.QualityIO)
FastqPhredWriter (class in Bio.SeqIO.QualityIO)
FastqSolexaIterator() (in module Bio.SeqIO.QualityIO)
FastqSolexaWriter (class in Bio.SeqIO.QualityIO)
FastTreeCommandline (class in Bio.Phylo.Applications)
FConsenseCommandline (class in Bio.Emboss.Applications)
FDNADistCommandline (class in Bio.Emboss.Applications)
FDNAParsCommandline (class in Bio.Emboss.Applications)
Feature (class in Bio.GenBank.Record)
(class in Bio.Graphics.GenomeDiagram)
FEATURE_END_MARKERS (Bio.GenBank.Scanner.EmblScanner attribute)
(Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.GenBank.Scanner.InsdcScanner attribute)
FEATURE_HEADER (Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.ImgtWriter attribute)
FEATURE_QUALIFIER_INDENT (Bio.GenBank.Scanner.EmblScanner attribute)
(Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.GenBank.Scanner.InsdcScanner attribute)
FEATURE_QUALIFIER_SPACER (Bio.GenBank.Scanner.EmblScanner attribute)
(Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.GenBank.Scanner.InsdcScanner attribute)
FEATURE_START_MARKERS (Bio.GenBank.Scanner.EmblScanner attribute)
(Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.GenBank.Scanner.InsdcScanner attribute)
FeatureLocation (class in Bio.SeqFeature)
FeatureParser (class in Bio.GenBank)
features() (BioSQL.BioSeq.DBSeqRecord property)
FeatureSet (class in Bio.Graphics.GenomeDiagram)
FeatureTable (class in Bio.SwissProt)
FeatureValueCleaner (class in Bio.GenBank.utils)
feed() (Bio.ExPASy.ScanProsite.Parser method)
(Bio.GenBank.Scanner.InsdcScanner method)
fetch_dbid_by_dbname() (BioSQL.BioSeqDatabase.Adaptor method)
fetch_motif_by_id() (Bio.motifs.jaspar.db.JASPAR5 method)
fetch_motifs() (Bio.motifs.jaspar.db.JASPAR5 method)
fetch_motifs_by_name() (Bio.motifs.jaspar.db.JASPAR5 method)
fetch_seqid_by_accession() (BioSQL.BioSeqDatabase.Adaptor method)
fetch_seqid_by_display_id() (BioSQL.BioSeqDatabase.Adaptor method)
fetch_seqid_by_identifier() (BioSQL.BioSeqDatabase.Adaptor method)
fetch_seqid_by_version() (BioSQL.BioSeqDatabase.Adaptor method)
fetch_seqids_by_accession() (BioSQL.BioSeqDatabase.Adaptor method)
ff() (Bio.Align.Applications.DialignCommandline property)
fff_rec (class in Bio.FSSP.fssp_rec)
fft() (Bio.Align.Applications.MafftCommandline property)
fgcolor() (Bio.KEGG.KGML.KGML_pathway.Graphics property)
fieldNames (Bio.PDB.internal_coords.AtomKey attribute)
fields (Bio.PDB.internal_coords.AtomKey attribute)
fileno() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
FileRecord (class in Bio.PopGen.GenePop.FileParser)
fill_chromosome() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method)
fill_header() (Bio.FSSP.FSSPHeader method)
filter() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
(in module Bio.FSSP.FSSPTools)
filtering_db() (Bio.Blast.Applications.NcbiblastnCommandline property)
finalize_structure() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
find() (Bio.Seq.Seq method)
find_any() (Bio.Phylo.BaseTree.TreeMixin method)
find_clades() (Bio.Phylo.BaseTree.TreeMixin method)
find_elements() (Bio.Phylo.BaseTree.TreeMixin method)
find_start() (Bio.GenBank.Scanner.InsdcScanner method)
find_states() (in module Bio.MarkovModel)
fit() (Bio.phenotype.phen_micro.WellRecord method)
(in module Bio.phenotype.pm_fitting)
fix() (Bio.Crystal.Crystal method)
fixedbranches() (Bio.Align.Applications.PrankCommandline property)
flag_disorder() (Bio.PDB.Atom.Atom method)
flag_disordered() (Bio.PDB.Residue.Residue method)
flexibility() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
float1_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method)
flush() (Bio.bgzf.BgzfWriter method)
fmodel() (Bio.Align.Applications.MafftCommandline property)
fmt_() (in module Bio.Blast.Record)
fn() (Bio.Align.Applications.DialignCommandline property)
FNeighborCommandline (class in Bio.Emboss.Applications)
fop() (Bio.Align.Applications.DialignCommandline property)
force() (Bio.Align.Applications.ClustalOmegaCommandline property)
format() (Bio.Align.MultipleSeqAlignment method)
(Bio.Align.PairwiseAlignment method)
(Bio.motifs.Motif method)
(Bio.Phylo.BaseTree.Tree method)
(Bio.SeqRecord.SeqRecord method)
(Bio.Sequencing.Applications.NovoalignCommandline property)
(Bio.SubsMat.SeqMat method)
format_alignment() (in module Bio.pairwise2)
format_label() (in module Bio.Phylo.CDAOIO)
format_output() (Bio.Restriction.PrintFormat.PrintFormat method)
format_phylip() (Bio.Phylo.TreeConstruction.DistanceMatrix method)
forward_algorithm() (Bio.HMM.DynamicProgramming.AbstractDPAlgorithms method)
forward_table (Bio.Data.CodonTable.CodonTable attribute)
forwardinput() (Bio.Emboss.Applications.Primer3Commandline property)
FProtDistCommandline (class in Bio.Emboss.Applications)
FProtParsCommandline (class in Bio.Emboss.Applications)
fracsample() (Bio.Emboss.Applications.FSeqBootCommandline property)
Fragment (class in Bio.PDB.FragmentMapper)
fragment() (Bio.Sequencing.Applications.NovoalignCommandline property)
FragmentMapper (class in Bio.PDB.FragmentMapper)
frame_shift_penalty() (Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
freqsfrom() (Bio.Emboss.Applications.FDNADistCommandline property)
FreqTable (class in Bio.SubsMat.FreqTable)
frequencies() (Bio.Phylo.Applications.PhymlCommandline property)
FrequencyPositionMatrix (class in Bio.motifs.matrix)
from_clade() (Bio.Phylo.BaseTree.Tree class method)
(Bio.Phylo.PhyloXML.Clade class method)
(Bio.Phylo.PhyloXML.Phylogeny class method)
from_hex() (Bio.Phylo.BaseTree.BranchColor class method)
from_msa() (Bio.codonalign.codonalignment.CodonAlignment class method)
from_name() (Bio.Phylo.BaseTree.BranchColor class method)
from_seq() (Bio.codonalign.codonseq.CodonSeq class method)
from_seqfeature() (Bio.Phylo.PhyloXML.ProteinDomain class method)
from_seqrecord() (Bio.Phylo.PhyloXML.Sequence class method)
from_string() (Bio.Phylo.CDAOIO.Parser class method)
(Bio.Phylo.NewickIO.Parser class method)
(Bio.Phylo.NeXMLIO.Parser class method)
from_tree() (Bio.Phylo.PhyloXML.Phylogeny class method)
FSeqBootCommandline (class in Bio.Emboss.Applications)
fsm() (Bio.Align.Applications.DialignCommandline property)
FSSPAlign (class in Bio.FSSP.FSSPTools)
FSSPAlignDict (class in Bio.FSSP)
FSSPAlignRec (class in Bio.FSSP)
FSSPHeader (class in Bio.FSSP)
FSSPMultAlign (class in Bio.FSSP.FSSPTools)
FSSPSumDict (class in Bio.FSSP)
FSSPSumRec (class in Bio.FSSP)
FTreeDistCommandline (class in Bio.Emboss.Applications)
full_translate() (Bio.codonalign.codonseq.CodonSeq method)
fullhelp() (Bio.Align.Applications.ClustalwCommandline property)
FuzznucCommandline (class in Bio.Emboss.Applications)
FuzzproCommandline (class in Bio.Emboss.Applications)
G
g() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
gafbyproteiniterator() (in module Bio.UniProt.GOA)
gafiterator() (in module Bio.UniProt.GOA)
gamma() (Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
gammacoefficient() (Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
gap() (Bio.Emboss.Applications.EInvertedCommandline property)
gap_consensus() (Bio.Align.AlignInfo.SummaryInfo method)
gap_extend() (Bio.Sequencing.Applications.NovoalignCommandline property)
gap_open() (Bio.Sequencing.Applications.NovoalignCommandline property)
gap_trigger() (Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
gapdist() (Bio.Align.Applications.ClustalwCommandline property)
gapext() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.PrankCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
gapextend() (Bio.Align.Applications.MuscleCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
gaplimit() (Bio.Emboss.Applications.PalindromeCommandline property)
gaponly() (Bio.Nexus.Nexus.Nexus method)
gapopen() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
gappenalty() (Bio.Emboss.Applications.Est2GenomeCommandline property)
gaprate() (Bio.Align.Applications.PrankCommandline property)
GB_BASE_INDENT (Bio.GenBank.Record.Record attribute)
GB_FEATURE_INDENT (Bio.GenBank.Record.Record attribute)
GB_FEATURE_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute)
GB_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute)
GB_LINE_LENGTH (Bio.GenBank.Record.Record attribute)
GB_OTHER_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute)
GB_SEQUENCE_INDENT (Bio.GenBank.Record.Record attribute)
GC() (in module Bio.SeqUtils)
GC123() (in module Bio.SeqUtils)
gc_content() (Bio.motifs.matrix.GenericPositionMatrix property)
(Bio.motifs.matrix.PositionSpecificScoringMatrix property)
GC_skew() (in module Bio.SeqUtils)
gcclamp() (Bio.Emboss.Applications.Primer3Commandline property)
gcg() (in module Bio.SeqUtils.CheckSum)
GckIterator (class in Bio.SeqIO.GckIO)
gen_acs() (Bio.PDB.internal_coords.Edron method)
gen_key() (Bio.PDB.internal_coords.Edron static method)
genafpair() (Bio.Align.Applications.MafftCommandline property)
GENBANK_INDENT (Bio.GenBank.Scanner.GenBankScanner attribute)
GENBANK_SPACER (Bio.GenBank.Scanner.GenBankScanner attribute)
GenBankCdsFeatureIterator (class in Bio.SeqIO.InsdcIO)
GenBankIterator (class in Bio.SeqIO.InsdcIO)
GenBankScanner (class in Bio.GenBank.Scanner)
GenBankWriter (class in Bio.SeqIO.InsdcIO)
GenePopController (class in Bio.PopGen.GenePop.Controller)
generate_index() (Bio.SeqUtils.CodonUsage.CodonAdaptationIndex method)
Generic_dbutils (class in BioSQL.DBUtils)
GenericPositionMatrix (class in Bio.motifs.matrix)
genes() (Bio.KEGG.KGML.KGML_pathway.Pathway property)
genome() (Bio.Emboss.Applications.Est2GenomeCommandline property)
get() (Bio.Align.substitution_matrices.Array method)
(Bio.Crystal.Crystal method)
(Bio.Data.CodonTable.AmbiguousForwardTable method)
get_acgt() (Bio.motifs.xms.XMSScanner method)
get_alignment_length() (Bio.Align.MultipleSeqAlignment method)
get_all_entries() (Bio.PDB.PDBList.PDBList method)
get_all_obsolete() (Bio.PDB.PDBList.PDBList method)
get_all_primary_ids() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
get_allele_frequency() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_alleles() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_alleles_all_pops() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_aln_length() (Bio.codonalign.codonalignment.CodonAlignment method)
get_altloc() (Bio.PDB.Atom.Atom method)
get_amino_acids_percent() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
get_angle() (Bio.PDB.internal_coords.IC_Residue method)
get_anisou() (Bio.PDB.Atom.Atom method)
get_area() (in module Bio.phenotype.pm_fitting)
get_array() (Bio.PDB.vectors.Vector method)
get_artemis_colorscheme() (Bio.Graphics.GenomeDiagram.ColorTranslator method)
get_atom() (Bio.PDB.Residue.Residue method)
get_atoms() (Bio.PDB.Chain.Chain method)
(Bio.PDB.Model.Model method)
(Bio.PDB.Residue.Residue method)
(Bio.PDB.Structure.Structure method)
get_avg_fis() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_avg_fst_pair() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_avg_fst_pair_locus() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_basic_info() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_bfactor() (Bio.PDB.Atom.Atom method)
get_blank_emissions() (Bio.HMM.MarkovModel.HiddenMarkovModel method)
get_blank_transitions() (Bio.HMM.MarkovModel.HiddenMarkovModel method)
get_ca_list() (Bio.PDB.Polypeptide.Polypeptide method)
get_chains() (Bio.PDB.Model.Model method)
(Bio.PDB.Structure.Structure method)
get_charge() (Bio.PDB.Atom.Atom method)
get_codon() (Bio.codonalign.codonseq.CodonSeq method)
get_codon_num() (Bio.codonalign.codonseq.CodonSeq method)
get_color_dict() (in module Bio.Graphics.ColorSpiral)
get_colors() (Bio.Graphics.ColorSpiral.ColorSpiral method)
(in module Bio.Graphics.ColorSpiral)
get_colorscheme() (Bio.Graphics.GenomeDiagram.ColorTranslator method)
get_column() (Bio.Align.AlignInfo.SummaryInfo method)
(Bio.phenotype.phen_micro.PlateRecord method)
get_coord() (Bio.PDB.Atom.Atom method)
get_coords() (Bio.PDB.FragmentMapper.Fragment method)
get_data() (Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.Nexus.Nodes.Node method)
get_dbutils() (in module BioSQL.DBUtils)
get_distance() (Bio.Phylo.TreeConstruction.DistanceCalculator method)
get_dn_ds_matrix() (Bio.codonalign.codonalignment.CodonAlignment method)
get_dn_ds_tree() (Bio.codonalign.codonalignment.CodonAlignment method)
get_drawn_levels() (Bio.Graphics.GenomeDiagram.Diagram method)
get_f_stats() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_feature() (Bio.Graphics.GenomeDiagram.Feature method)
get_features() (Bio.Graphics.GenomeDiagram.FeatureSet method)
get_fis() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_from_decoded() (in module Bio.PDB.mmtf)
get_full_id() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.Entity method)
get_full_rf_table() (Bio.codonalign.codonseq.CodonSeq method)
get_fullname() (Bio.PDB.Atom.Atom method)
get_genotype_count() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_graphs() (Bio.Graphics.GenomeDiagram.GraphSet method)
get_header() (Bio.PDB.PDBParser.PDBParser method)
get_heterozygosity_info() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_id() (Bio.Nexus.Nodes.Node method)
(Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.FragmentMapper.Fragment method)
get_ids() (Bio.Graphics.GenomeDiagram.FeatureSet method)
(Bio.Graphics.GenomeDiagram.GraphSet method)
(Bio.Graphics.GenomeDiagram.Track method)
get_indiv() (in module Bio.PopGen.GenePop)
(in module Bio.PopGen.GenePop.LargeFileParser)
get_individual() (Bio.PopGen.GenePop.FileParser.FileRecord method)
get_init_rms() (Bio.PDB.QCPSuperimposer.QCPSuperimposer method)
(Bio.SVDSuperimposer.SVDSuperimposer method)
get_iterator() (Bio.PDB.Entity.Entity method)
(Bio.PDB.StructureAlignment.StructureAlignment method)
get_KGML() (Bio.KEGG.KGML.KGML_pathway.Pathway method)
get_length() (Bio.PDB.internal_coords.Hedron method)
(Bio.PDB.internal_coords.IC_Residue method)
get_level() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.Entity method)
get_levels() (Bio.Graphics.GenomeDiagram.Diagram method)
get_list() (Bio.PDB.Entity.Entity method)
get_maps() (Bio.PDB.StructureAlignment.StructureAlignment method)
get_markov_model() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
get_models() (Bio.PDB.Structure.Structure method)
get_multilocus_f_stats() (Bio.PopGen.GenePop.EasyController.EasyController method)
get_name() (Bio.PDB.Atom.Atom method)
get_node_info() (Bio.Phylo.CDAOIO.Parser method)
get_nonterminals() (Bio.Phylo.BaseTree.TreeMixin method)
get_occupancy() (Bio.PDB.Atom.Atom method)
get_original_taxon_order() (Bio.Nexus.Nexus.Nexus method)
get_parent() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
get_path() (Bio.Phylo.BaseTree.TreeMixin method)
get_phi_psi_list() (Bio.PDB.Polypeptide.Polypeptide method)
get_prev() (Bio.Nexus.Nodes.Node method)
get_prodoc_entry() (in module Bio.ExPASy)
get_property_value() (Bio.motifs.xms.XMSScanner method)
get_prosite_entry() (in module Bio.ExPASy)
get_prosite_raw() (in module Bio.ExPASy)
get_qresult_id() (Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer method)
(Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer method)
(Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer method)
get_radius() (Bio.PDB.Atom.Atom method)
get_raw() (Bio.phenotype.phen_micro.WellRecord method)
(Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer method)
(Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer method)
(Bio.SearchIO.BlatIO.BlatPslIndexer method)
(Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer method)
(Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer method)
(Bio.SearchIO.FastaIO.FastaM10Indexer method)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer method)
get_recent_changes() (Bio.PDB.PDBList.PDBList method)
get_residue() (Bio.Align.AlignInfo.PSSM method)
get_residues() (Bio.PDB.Chain.Chain method)
(Bio.PDB.Model.Model method)
(Bio.PDB.Structure.Structure method)
get_resname() (Bio.PDB.Residue.Residue method)
get_resname_list() (Bio.PDB.FragmentMapper.Fragment method)
get_rms() (Bio.PDB.QCPSuperimposer.QCPSuperimposer method)
(Bio.SVDSuperimposer.SVDSuperimposer method)
get_rotran() (Bio.PDB.QCPSuperimposer.QCPSuperimposer method)
(Bio.SVDSuperimposer.SVDSuperimposer method)
get_row() (Bio.phenotype.phen_micro.PlateRecord method)
get_score() (Bio.Phylo.TreeConstruction.ParsimonyScorer method)
(Bio.Phylo.TreeConstruction.Scorer method)
get_segid() (Bio.PDB.Residue.Residue method)
get_segment_info() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method)
get_seq() (Bio.PDB.PSEA.PSEA method)
get_Seq_by_acc() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
get_Seq_by_id() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
get_Seq_by_primary_id() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
get_Seq_by_ver() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
get_seqres_file() (Bio.PDB.PDBList.PDBList method)
get_Seqs_by_acc() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
get_sequence() (Bio.PDB.Polypeptide.Polypeptide method)
get_serial_number() (Bio.PDB.Atom.Atom method)
get_sets() (Bio.Graphics.GenomeDiagram.Track method)
get_sigatm() (Bio.PDB.Atom.Atom method)
get_signals() (Bio.phenotype.phen_micro.WellRecord method)
get_siguij() (Bio.PDB.Atom.Atom method)
get_spherical_coordinates() (in module Bio.PDB.vectors)
get_spliced() (Bio.AlignIO.MafIO.MafIndex method)
get_sprot_raw() (in module Bio.ExPASy)
get_start_end() (in module Bio.Nexus.Nexus)
get_startpos() (Bio.PDB.internal_coords.IC_Residue method)
get_status_list() (Bio.PDB.PDBList.PDBList static method)
get_structure() (Bio.PDB.MMCIFParser.FastMMCIFParser method)
(Bio.PDB.MMCIFParser.MMCIFParser method)
(Bio.PDB.mmtf.MMTFParser static method)
(Bio.PDB.PDBParser.PDBParser method)
(Bio.PDB.StructureBuilder.StructureBuilder method)
get_structure_from_url() (Bio.PDB.mmtf.MMTFParser static method)
get_subseq_as_string() (BioSQL.BioSeqDatabase.Adaptor method)
get_succ() (Bio.Nexus.Nodes.Node method)
get_support() (in module Bio.Phylo.Consensus)
get_surface() (in module Bio.PDB.ResidueDepth)
get_tau_list() (Bio.PDB.Polypeptide.Polypeptide method)
get_taxa() (Bio.Nexus.Trees.Tree method)
get_temp_imagefilename() (in module Bio.Graphics.KGML_vis)
get_terminals() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
get_text() (Bio.motifs.xms.XMSScanner method)
get_theta_list() (Bio.PDB.Polypeptide.Polypeptide method)
get_times() (Bio.phenotype.phen_micro.WellRecord method)
get_tracks() (Bio.Graphics.GenomeDiagram.Diagram method)
get_trailer() (Bio.PDB.PDBParser.PDBParser method)
get_transformed() (Bio.PDB.QCPSuperimposer.QCPSuperimposer method)
(Bio.SVDSuperimposer.SVDSuperimposer method)
get_unique_parents() (in module Bio.PDB.Selection)
get_unpacked_list() (Bio.PDB.Chain.Chain method)
(Bio.PDB.Residue.Residue method)
get_vector() (Bio.PDB.Atom.Atom method)
getAscendent() (Bio.SCOP.Node method)
getAscendentFromSQL() (Bio.SCOP.Scop method)
getAstralDomainsFromFile() (Bio.SCOP.Astral method)
getAstralDomainsFromSQL() (Bio.SCOP.Astral method)
getAtoms() (Bio.SCOP.Raf.SeqMap method)
getChildren() (Bio.SCOP.Node method)
getDescendents() (Bio.SCOP.Node method)
getDescendentsFromSQL() (Bio.SCOP.Scop method)
getDomainBySid() (Bio.SCOP.Scop method)
getDomainFromSQL() (Bio.SCOP.Scop method)
getDomains() (Bio.SCOP.Scop method)
getNodeBySunid() (Bio.SCOP.Scop method)
getParent() (Bio.SCOP.Node method)
getRoot() (Bio.SCOP.Scop method)
getSeq() (Bio.SCOP.Astral method)
getSeqBySid() (Bio.SCOP.Astral method)
getSeqMap() (Bio.SCOP.Raf.SeqMapIndex method)
gi_mask() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
gi_mask_name() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
gilist() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
global_dtd_dir (Bio.Entrez.Parser.DataHandler attribute)
global_xsd_dir (Bio.Entrez.Parser.DataHandler attribute)
globalpair() (Bio.Align.Applications.MafftCommandline property)
gly_Cbeta (Bio.PDB.internal_coords.IC_Residue attribute)
gompertz() (in module Bio.phenotype.pm_fitting)
good_bases() (Bio.Sequencing.Applications.NovoalignCommandline property)
gpa_iterator() (in module Bio.UniProt.GOA)
gpi_iterator() (in module Bio.UniProt.GOA)
Graph (class in Bio.Pathway.Rep.Graph)
GraphData (class in Bio.Graphics.GenomeDiagram)
Graphics (class in Bio.KEGG.KGML.KGML_pathway)
GraphSet (class in Bio.Graphics.GenomeDiagram)
gravy() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
green() (Bio.Phylo.PhyloXMLIO.Writer method)
group() (Bio.Align.Applications.MuscleCommandline property)
grouping_constraint() (Bio.Phylo.Applications.RaxmlCommandline property)
groupsize() (Bio.Align.Applications.MafftCommandline property)
gtr() (Bio.Phylo.Applications.FastTreeCommandline property)
gtrfreq() (Bio.Phylo.Applications.FastTreeCommandline property)
gtrrates() (Bio.Phylo.Applications.FastTreeCommandline property)
guess_lag() (in module Bio.phenotype.pm_fitting)
guess_plateau() (in module Bio.phenotype.pm_fitting)
guidetree_in() (Bio.Align.Applications.ClustalOmegaCommandline property)
guidetree_out() (Bio.Align.Applications.ClustalOmegaCommandline property)
H
h() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbimakeblastdbCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
H() (Bio.Sequencing.Applications.BwaMemCommandline property)
h() (Bio.Sequencing.Applications.SamtoolsCatCommandline property)
(Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
H() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
h() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
handle_motif() (Bio.motifs.xms.XMSScanner method)
handleMissingDocumentDefinition() (Bio.Entrez.Parser.DataHandler method)
has_id() (Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.Entity method)
has_key() (Bio.Crystal.Crystal method)
has_support() (Bio.Nexus.Trees.Tree method)
hash_index() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
hashedDomainsByEv() (Bio.SCOP.Astral method)
hashedDomainsById() (Bio.SCOP.Astral method)
header (Bio.Wise.dnal.Statistics attribute)
Header (class in Bio.Blast.Record)
HEADER_WIDTH (Bio.GenBank.Scanner.EmblScanner attribute)
(Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.GenBank.Scanner.InsdcScanner attribute)
(Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
(Bio.SeqIO.InsdcIO.ImgtWriter attribute)
Hedron (class in Bio.PDB.internal_coords)
HedronMatchError
height() (Bio.KEGG.KGML.KGML_pathway.Graphics property)
helixendin() (Bio.Align.Applications.ClustalwCommandline property)
helixendout() (Bio.Align.Applications.ClustalwCommandline property)
helixgap() (Bio.Align.Applications.ClustalwCommandline property)
help() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.ClustalwCommandline property)
(Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbimakeblastdbCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
(Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
Hetero (class in Bio.Crystal)
hgapresidues() (Bio.Align.Applications.ClustalwCommandline property)
Hhsuite2TextParser (class in Bio.SearchIO.HHsuiteIO.hhsuite2_text)
HiddenMarkovModel (class in Bio.HMM.MarkovModel)
hit_coverage() (Bio.Compass.Record method)
hmm_as_hit (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser attribute)
(Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter attribute)
(Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser attribute)
(Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter attribute)
hmm_input() (Bio.Align.Applications.ClustalOmegaCommandline property)
Hmmer2TextIndexer (class in Bio.SearchIO.HmmerIO.hmmer2_text)
Hmmer2TextParser (class in Bio.SearchIO.HmmerIO.hmmer2_text)
Hmmer3DomtabHmmhitIndexer (class in Bio.SearchIO.HmmerIO.hmmer3_domtab)
Hmmer3DomtabHmmhitParser (class in Bio.SearchIO.HmmerIO.hmmer3_domtab)
Hmmer3DomtabHmmhitWriter (class in Bio.SearchIO.HmmerIO.hmmer3_domtab)
Hmmer3DomtabHmmqueryIndexer (class in Bio.SearchIO.HmmerIO.hmmer3_domtab)
Hmmer3DomtabHmmqueryParser (class in Bio.SearchIO.HmmerIO.hmmer3_domtab)
Hmmer3DomtabHmmqueryWriter (class in Bio.SearchIO.HmmerIO.hmmer3_domtab)
Hmmer3TabIndexer (class in Bio.SearchIO.HmmerIO.hmmer3_tab)
Hmmer3TabParser (class in Bio.SearchIO.HmmerIO.hmmer3_tab)
Hmmer3TabWriter (class in Bio.SearchIO.HmmerIO.hmmer3_tab)
Hmmer3TextIndexer (class in Bio.SearchIO.HmmerIO.hmmer3_text)
Hmmer3TextParser (class in Bio.SearchIO.HmmerIO.hmmer3_text)
homog_rot_mtx() (in module Bio.PDB.vectors)
homog_scale_mtx() (in module Bio.PDB.vectors)
homog_trans_mtx() (in module Bio.PDB.vectors)
homopolymer() (Bio.Sequencing.Applications.NovoalignCommandline property)
HSExposureCA (class in Bio.PDB.HSExposure)
HSExposureCB (class in Bio.PDB.HSExposure)
HSP (class in Bio.Blast.Record)
html() (Bio.Align.Applications.MuscleCommandline property)
(Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
htmlout() (Bio.Align.Applications.MuscleCommandline property)
hybridprobe() (Bio.Emboss.Applications.Primer3Commandline property)
hydro() (Bio.Align.Applications.MuscleCommandline property)
hydrofactor() (Bio.Align.Applications.MuscleCommandline property)
I
I() (Bio.Sequencing.Applications.BwaAlignCommandline property)
i() (Bio.Sequencing.Applications.BwaAlignCommandline property)
I() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
i() (Bio.Sequencing.Applications.SamtoolsTargetcutCommandline property)
I() (Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline property)
IC_Chain (class in Bio.PDB.internal_coords)
IC_duplicate() (in module Bio.PDB.ic_rebuild)
IC_Residue (class in Bio.PDB.internal_coords)
icode() (Bio.PDB.internal_coords.AtomKey.fieldsDef property)
Id (class in Bio.Phylo.PhyloXML)
id() (Bio.KEGG.KGML.KGML_pathway.Component property)
(Bio.KEGG.KGML.KGML_pathway.Entry property)
(Bio.KEGG.KGML.KGML_pathway.Reaction property)
(Bio.PDB.Entity.Entity property)
(Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
id_width (Bio.AlignIO.PhylipIO.PhylipIterator attribute)
identity_fraction() (Bio.Wise.dnal.Statistics method)
identity_match (class in Bio.pairwise2)
IepCommandline (class in Bio.Emboss.Applications)
IgIterator (class in Bio.SeqIO.IgIO)
ignore_msa_master() (Bio.Blast.Applications.NcbipsiblastCommandline property)
illumina_13() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
ImgtIterator (class in Bio.SeqIO.InsdcIO)
ImgtWriter (class in Bio.SeqIO.InsdcIO)
import_search_strategy() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
in1() (Bio.Align.Applications.MuscleCommandline property)
in2() (Bio.Align.Applications.MuscleCommandline property)
in_bam() (Bio.Sequencing.Applications.SamtoolsPhaseCommandline property)
(Bio.Sequencing.Applications.SamtoolsTargetcutCommandline property)
in_msa() (Bio.Blast.Applications.NcbipsiblastCommandline property)
in_pssm() (Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
includedregion() (Bio.Emboss.Applications.Primer3Commandline property)
inclusion_ethresh() (Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
Indent (Bio.Restriction.PrintFormat.PrintFormat attribute)
Index (class in Bio.SCOP.Cla)
index() (Bio.Crystal.Chain method)
(Bio.SCOP.Raf.SeqMap method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(in module Bio.SearchIO)
(in module Bio.SeqIO)
index_db() (in module Bio.SearchIO)
(in module Bio.SeqIO)
index_name() (Bio.Blast.Applications.NcbiblastnCommandline property)
index_to_one() (in module Bio.PDB.Polypeptide)
index_to_three() (in module Bio.PDB.Polypeptide)
infile() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.MSAProbsCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Sequencing.Applications.BwaIndexCommandline property)
infmt() (Bio.Align.Applications.ClustalOmegaCommandline property)
information_content() (Bio.Align.AlignInfo.SummaryInfo method)
init_atom() (Bio.PDB.StructureBuilder.StructureBuilder method)
init_atom_coords() (Bio.PDB.internal_coords.IC_Chain method)
init_chain() (Bio.PDB.StructureBuilder.StructureBuilder method)
init_edra() (Bio.PDB.internal_coords.IC_Chain method)
init_model() (Bio.PDB.StructureBuilder.StructureBuilder method)
init_residue() (Bio.PDB.StructureBuilder.StructureBuilder method)
init_seg() (Bio.PDB.StructureBuilder.StructureBuilder method)
init_structure() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
(Bio.PDB.StructureBuilder.StructureBuilder method)
input() (Bio.Align.Applications.DialignCommandline property)
(Bio.Align.Applications.MafftCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
(Bio.Align.Applications.ProbconsCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
(Bio.Phylo.Applications.PhymlCommandline property)
(Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline property)
(Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline property)
input1() (Bio.Align.Applications.MafftCommandline property)
input_bam() (Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
(Bio.Sequencing.Applications.SamtoolsIdxstatsCommandline property)
(Bio.Sequencing.Applications.SamtoolsIndexCommandline property)
input_file() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
(Bio.Sequencing.Applications.SamtoolsFixmateCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
(Bio.Sequencing.Applications.SamtoolsRmdupCommandline property)
(Bio.Sequencing.Applications.SamtoolsViewCommandline property)
input_tree() (Bio.Phylo.Applications.PhymlCommandline property)
input_type() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
inputorder() (Bio.Align.Applications.MafftCommandline property)
InputRecord (class in Bio.Emboss.PrimerSearch)
InsdcScanner (class in Bio.GenBank.Scanner)
insert() (Bio.Crystal.Chain method)
(Bio.PDB.Entity.Entity method)
(Bio.Seq.MutableSeq method)
insert_gap() (Bio.Nexus.Nexus.Nexus method)
instability_index() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
Instance (class in Bio.motifs.meme)
Instances (class in Bio.motifs)
int255_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method)
IntegerElement (class in Bio.Entrez.Parser)
integers (Bio.ExPASy.ScanProsite.ContentHandler attribute)
Interaction (class in Bio.Pathway)
interactions() (Bio.Pathway.Network method)
INTERNAL_FEATURE_FORMAT (Bio.GenBank.Record.Record attribute)
INTERNAL_FORMAT (Bio.GenBank.Record.Record attribute)
internal_to_atom_coordinates() (Bio.PDB.Chain.Chain method)
(Bio.PDB.internal_coords.IC_Chain method)
(Bio.PDB.Model.Model method)
(Bio.PDB.Structure.Structure method)
InterproscanXmlParser (class in Bio.SearchIO.InterproscanIO.interproscan_xml)
intree() (Bio.Phylo.Applications.FastTreeCommandline property)
intree1() (Bio.Phylo.Applications.FastTreeCommandline property)
intreefile() (Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
intronpenalty() (Bio.Emboss.Applications.Est2GenomeCommandline property)
invarcoefficient() (Bio.Emboss.Applications.FProtDistCommandline property)
invarfrac() (Bio.Emboss.Applications.FDNADistCommandline property)
invert() (Bio.Nexus.Nexus.Nexus method)
ir() (Bio.Align.Applications.ProbconsCommandline property)
is_aa() (in module Bio.PDB.Polypeptide)
is_backbone() (Bio.PDB.internal_coords.Edron method)
is_bifurcating() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
is_compatible() (Bio.Nexus.Trees.Tree method)
is_disordered() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Residue.Residue method)
is_identical() (Bio.Nexus.Trees.Tree method)
is_internal() (Bio.Nexus.Trees.Tree method)
is_monophyletic() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
is_parent_of() (Bio.Nexus.Nodes.Chain method)
(Bio.Phylo.BaseTree.TreeMixin method)
is_preterminal() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
is_reactant() (Bio.KEGG.KGML.KGML_pathway.Entry property)
is_terminal() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.Clade method)
(Bio.Phylo.BaseTree.Tree method)
isatty() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
isDomainInEv() (Bio.SCOP.Astral method)
isDomainInId() (Bio.SCOP.Astral method)
isoelectric_point() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
IsoelectricPoint (class in Bio.SeqUtils.IsoelectricPoint)
isprofile() (Bio.Align.Applications.ClustalOmegaCommandline property)
itemindex() (in module Bio.MarkovModel)
items() (Bio.Align.substitution_matrices.Array method)
(Bio.Crystal.Crystal method)
(Bio.Phylo.PhyloXML.Events method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
iterate() (Bio.SeqIO.AbiIO.AbiIterator method)
(Bio.SeqIO.FastaIO.FastaIterator method)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)
(Bio.SeqIO.IgIO.IgIterator method)
(Bio.SeqIO.NibIO.NibIterator method)
(Bio.SeqIO.PdbIO.PdbSeqresIterator method)
(Bio.SeqIO.PirIO.PirIterator method)
(Bio.SeqIO.QualityIO.FastqPhredIterator method)
(Bio.SeqIO.QualityIO.QualPhredIterator method)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator method)
(Bio.SeqIO.SffIO.SffIterator method)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator method)
(Bio.SeqIO.TabIO.TabIterator method)
(Bio.SeqIO.XdnaIO.XdnaIterator method)
iteration() (Bio.Align.Applications.ClustalwCommandline property)
iterations() (Bio.Align.Applications.ClustalOmegaCommandline property)
iterative_refinement() (Bio.Align.Applications.MSAProbsCommandline property)
Iterator (class in Bio.GenBank)
iw() (Bio.Align.Applications.DialignCommandline property)
J
JASPAR5 (class in Bio.motifs.jaspar.db)
jitter() (Bio.Graphics.ColorSpiral.ColorSpiral property)
join() (Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
JsonIterator() (in module Bio.phenotype.phen_micro)
JsonWriter (class in Bio.phenotype.phen_micro)
jtt() (Bio.Align.Applications.MafftCommandline property)
jumble() (Bio.Emboss.Applications.FNeighborCommandline property)
jusweights() (Bio.Emboss.Applications.FSeqBootCommandline property)
K
k() (Bio.Sequencing.Applications.BwaAlignCommandline property)
(Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.SamtoolsPhaseCommandline property)
kappa() (Bio.Align.Applications.PrankCommandline property)
kcluster() (Bio.Cluster.Record method)
(in module Bio.Cluster)
kegg_conv() (in module Bio.KEGG.REST)
kegg_find() (in module Bio.KEGG.REST)
kegg_get() (in module Bio.KEGG.REST)
kegg_info() (in module Bio.KEGG.REST)
kegg_link() (in module Bio.KEGG.REST)
kegg_list() (in module Bio.KEGG.REST)
keys() (Bio.Align.substitution_matrices.Array method)
(Bio.Crystal.Crystal method)
(Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method)
(Bio.Phylo.PhyloXML.Events method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
keys_to_process (Bio.GenBank.utils.FeatureValueCleaner attribute)
KGMLCanvas (class in Bio.Graphics.KGML_vis)
KGMLParser (class in Bio.KEGG.KGML.KGML_parser)
kill() (Bio.Nexus.Nodes.Chain method)
kimura() (Bio.Align.Applications.ClustalwCommandline property)
kmedoids() (in module Bio.Cluster)
kNN (class in Bio.kNN)
KnownStateTrainer (class in Bio.HMM.Trainer)
ktuple() (Bio.Align.Applications.ClustalwCommandline property)
L
l() (Bio.Sequencing.Applications.BwaAlignCommandline property)
L() (Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
l() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
(Bio.Sequencing.Applications.SamtoolsViewCommandline property)
labels() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
ladderize() (Bio.Phylo.BaseTree.TreeMixin method)
last_id() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.DBUtils.Generic_dbutils method)
(BioSQL.DBUtils.Mysql_dbutils method)
lat() (Bio.Phylo.PhyloXMLIO.Writer method)
lcase_masking() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
lcc_mult() (in module Bio.SeqUtils.lcc)
lcc_simp() (in module Bio.SeqUtils.lcc)
le() (Bio.Align.Applications.MuscleCommandline property)
left_multiply() (Bio.PDB.vectors.Vector method)
len12() (Bio.PDB.internal_coords.Hedron property)
len23() (Bio.PDB.internal_coords.Hedron property)
lep() (Bio.Align.Applications.MafftCommandline property)
letter_annotations() (Bio.SeqRecord.SeqRecord property)
LETTERS_PER_BLOCK (Bio.SeqIO.InsdcIO.EmblWriter attribute)
LETTERS_PER_LINE (Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
LEXP() (Bio.Align.Applications.MafftCommandline property)
lexp() (Bio.Align.Applications.MafftCommandline property)
lgs() (Bio.Align.Applications.DialignCommandline property)
lgs_t() (Bio.Align.Applications.DialignCommandline property)
line_length() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
LineDistribution (class in Bio.Graphics.Distribution)
linesize (Bio.Restriction.PrintFormat.PrintFormat attribute)
link() (Bio.Nexus.Nodes.Chain method)
link_dihedra() (Bio.PDB.internal_coords.IC_Residue method)
link_residues() (Bio.PDB.internal_coords.IC_Chain method)
list_ambiguous_codons() (in module Bio.Data.CodonTable)
list_any_ids() (BioSQL.BioSeqDatabase.Adaptor method)
list_biodatabase_names() (BioSQL.BioSeqDatabase.Adaptor method)
list_bioentry_display_ids() (BioSQL.BioSeqDatabase.Adaptor method)
list_bioentry_ids() (BioSQL.BioSeqDatabase.Adaptor method)
list_possible_proteins() (in module Bio.Data.CodonTable)
ListElement (class in Bio.Entrez.Parser)
lmax() (Bio.Align.Applications.DialignCommandline property)
lo() (Bio.Align.Applications.DialignCommandline property)
load() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
(in module Bio.Align.substitution_matrices)
(in module Bio.MarkovModel)
load_database_sql() (BioSQL.BioSeqDatabase.DBServer method)
load_PIC() (Bio.PDB.internal_coords.IC_Residue method)
load_seqrecord() (BioSQL.Loader.DatabaseLoader method)
local_dtd_dir (Bio.Entrez.Parser.DataHandler attribute)
local_xsd_dir (Bio.Entrez.Parser.DataHandler attribute)
localpair() (Bio.Align.Applications.MafftCommandline property)
location() (Bio.Phylo.PhyloXMLIO.Writer method)
location_operator() (Bio.SeqFeature.SeqFeature property)
LocationParserError
log() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
log_likelihood() (Bio.HMM.Trainer.AbstractTrainer method)
log_odds() (Bio.motifs.matrix.PositionWeightMatrix method)
loga() (Bio.Align.Applications.MuscleCommandline property)
LogDPAlgorithms (class in Bio.HMM.DynamicProgramming)
logfile() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
logistic() (in module Bio.phenotype.pm_fitting)
LogisticRegression (class in Bio.LogisticRegression)
LogOddsMatrix (class in Bio.SubsMat)
long() (Bio.Phylo.PhyloXMLIO.Writer method)
long_version() (Bio.Align.Applications.ClustalOmegaCommandline property)
longseq() (Bio.Align.Applications.PrankCommandline property)
lookup() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
loopgap() (Bio.Align.Applications.ClustalwCommandline property)
LOP() (Bio.Align.Applications.MafftCommandline property)
lop() (Bio.Align.Applications.MafftCommandline property)
losses() (Bio.Phylo.PhyloXMLIO.Writer method)
lower() (Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqRecord.SeqRecord method)
lowess() (in module Bio.Statistics.lowess)
lstrip() (Bio.Seq.Seq method)
lysinemodified() (Bio.Emboss.Applications.IepCommandline property)
M
m() (Bio.Align.Applications.PrankCommandline property)
M() (Bio.Sequencing.Applications.BwaAlignCommandline property)
(Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
m() (Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline property)
(Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline property)
m2rotaxis() (in module Bio.PDB.vectors)
ma() (Bio.Align.Applications.DialignCommandline property)
MafftCommandline (class in Bio.Align.Applications)
MafIndex (class in Bio.AlignIO.MafIO)
MafIterator() (in module Bio.AlignIO.MafIO)
MafWriter (class in Bio.AlignIO.MafIO)
main() (in module Bio.Wise)
(in module Bio.Wise.dnal)
(in module Bio.Wise.psw)
majority_consensus() (in module Bio.Phylo.Consensus)
make_back_table() (in module Bio.Data.CodonTable)
make_dssp_dict() (in module Bio.PDB.DSSP)
make_entropy() (Bio.SubsMat.SeqMat method)
make_format() (Bio.Restriction.PrintFormat.PrintFormat method)
make_log_odds_matrix() (in module Bio.SubsMat)
make_table() (in module Bio.SeqUtils.MeltingTemp)
make_virtual_offset() (in module Bio.bgzf)
makematrix() (Bio.Phylo.Applications.FastTreeCommandline property)
maps() (Bio.KEGG.KGML.KGML_pathway.Pathway property)
MarkovModel (class in Bio.MarkovModel)
MarkovModelBuilder (class in Bio.HMM.MarkovModel)
mask() (Bio.Align.Applications.DialignCommandline property)
(Bio.motifs.Motif property)
mask_data() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
mask_desc() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
mask_id() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
mat() (Bio.Align.Applications.DialignCommandline property)
mat_thr() (Bio.Align.Applications.DialignCommandline property)
match() (Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
matches() (in module Bio.Phylo.NeXMLIO)
mate_file() (Bio.Sequencing.Applications.BwaBwaswCommandline property)
matinitsize() (Bio.Align.Applications.PrankCommandline property)
matresize() (Bio.Align.Applications.PrankCommandline property)
matrix() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
matrixtype() (Bio.Emboss.Applications.FNeighborCommandline property)
MauveIterator (class in Bio.AlignIO.MauveIO)
MauveWriter (class in Bio.AlignIO.MauveIO)
max() (Bio.motifs.matrix.PositionSpecificScoringMatrix property)
max_file_sz() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
max_guidetree_iterations() (Bio.Align.Applications.ClustalOmegaCommandline property)
max_hmm_iterations() (Bio.Align.Applications.ClustalOmegaCommandline property)
max_hsps() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
max_hsps_per_subject() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
max_intron_length() (Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
max_link() (Bio.Align.Applications.DialignCommandline property)
max_target_seqs() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
maxbranches() (Bio.Align.Applications.PrankCommandline property)
maxdiagbreak() (Bio.Align.Applications.MuscleCommandline property)
maxdifftm() (Bio.Emboss.Applications.Primer3Commandline property)
maxdiv() (Bio.Align.Applications.ClustalwCommandline property)
MaxEntropy (class in Bio.MaxEntropy)
maxgc() (Bio.Emboss.Applications.Primer3Commandline property)
maxhours() (Bio.Align.Applications.MuscleCommandline property)
maximum() (Bio.Phylo.PhyloXMLIO.Writer method)
maxiterate() (Bio.Align.Applications.MafftCommandline property)
maxiters() (Bio.Align.Applications.MuscleCommandline property)
maxmispriming() (Bio.Emboss.Applications.Primer3Commandline property)
maxnumseq() (Bio.Align.Applications.ClustalOmegaCommandline property)
maxpallen() (Bio.Emboss.Applications.PalindromeCommandline property)
MaxPeptideBond (Bio.PDB.internal_coords.IC_Chain attribute)
maxpolyx() (Bio.Emboss.Applications.Primer3Commandline property)
maxrepeat() (Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
maxseqlen() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.ClustalwCommandline property)
MaxSize (Bio.Restriction.PrintFormat.PrintFormat attribute)
maxsize() (Bio.Emboss.Applications.Primer3Commandline property)
maxtm() (Bio.Emboss.Applications.Primer3Commandline property)
maxtrees() (Bio.Align.Applications.MuscleCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
mean() (Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.motifs.matrix.PositionSpecificScoringMatrix method)
memsave() (Bio.Align.Applications.MafftCommandline property)
merge_with_support() (Bio.Nexus.Trees.Tree method)
method() (Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
methods (Bio.Phylo.TreeConstruction.DistanceTreeConstructor attribute)
min() (Bio.motifs.matrix.PositionSpecificScoringMatrix property)
min_dist() (in module Bio.PDB.ResidueDepth)
min_link() (Bio.Align.Applications.DialignCommandline property)
min_raw_gapped_score() (Bio.Blast.Applications.NcbiblastnCommandline property)
minbestcolscore() (Bio.Align.Applications.MuscleCommandline property)
mingc() (Bio.Emboss.Applications.Primer3Commandline property)
minimum() (Bio.Phylo.PhyloXMLIO.Writer method)
minpallen() (Bio.Emboss.Applications.PalindromeCommandline property)
minrepeat() (Bio.Emboss.Applications.ETandemCommandline property)
minscore() (Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
minsize() (Bio.Emboss.Applications.Primer3Commandline property)
minsmoothscore() (Bio.Align.Applications.MuscleCommandline property)
mintm() (Bio.Emboss.Applications.Primer3Commandline property)
miRNA() (Bio.Sequencing.Applications.NovoalignCommandline property)
mishyblibraryfile() (Bio.Emboss.Applications.Primer3Commandline property)
mismatch() (Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
mismatchpercent() (Bio.Emboss.Applications.PrimerSearchCommandline property)
mispriminglibraryfile() (Bio.Emboss.Applications.Primer3Commandline property)
MissingAtomError
MissingExternalDependencyError
MissingPythonDependencyError
mktest() (in module Bio.codonalign.codonalignment)
ml_estimator() (Bio.HMM.Trainer.AbstractTrainer method)
mlacc() (Bio.Phylo.Applications.FastTreeCommandline property)
mlfrac() (Bio.Emboss.Applications.FConsenseCommandline property)
mllen() (Bio.Phylo.Applications.FastTreeCommandline property)
mlnni() (Bio.Phylo.Applications.FastTreeCommandline property)
MMCIF2Dict (class in Bio.PDB.MMCIF2Dict)
MMCIFIO (class in Bio.PDB.mmcifio)
MMCIFParser (class in Bio.PDB.MMCIFParser)
MMTFIO (class in Bio.PDB.mmtf.mmtfio)
MMTFParser (class in Bio.PDB.mmtf)
mode() (Bio.Align.Applications.TCoffeeCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
Model (class in Bio.PDB.Model)
model() (Bio.Phylo.Applications.PhymlCommandline property)
(Bio.Phylo.Applications.RaxmlCommandline property)
models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute)
modify() (Bio.motifs.thresholds.ScoreDistribution method)
module
Bio
Bio.Affy
Bio.Affy.CelFile
Bio.Align
Bio.Align.AlignInfo
Bio.Align.Applications
Bio.Align.substitution_matrices
Bio.AlignIO
Bio.AlignIO.ClustalIO
Bio.AlignIO.EmbossIO
Bio.AlignIO.FastaIO
Bio.AlignIO.Interfaces
Bio.AlignIO.MafIO
Bio.AlignIO.MauveIO
Bio.AlignIO.MsfIO
Bio.AlignIO.NexusIO
Bio.AlignIO.PhylipIO
Bio.AlignIO.StockholmIO
Bio.Alphabet
Bio.Application
Bio.bgzf
Bio.Blast
Bio.Blast.Applications
Bio.Blast.NCBIWWW
Bio.Blast.NCBIXML
Bio.Blast.ParseBlastTable
Bio.Blast.Record
Bio.CAPS
Bio.Cluster
Bio.codonalign
Bio.codonalign.chisq
Bio.codonalign.codonalignment
Bio.codonalign.codonseq
Bio.Compass
Bio.Crystal
Bio.Data
Bio.Data.CodonTable
Bio.Data.IUPACData
Bio.Data.SCOPData
Bio.Emboss
Bio.Emboss.Applications
Bio.Emboss.Primer3
Bio.Emboss.PrimerSearch
Bio.Entrez
Bio.Entrez.Parser
Bio.ExPASy
Bio.ExPASy.cellosaurus
Bio.ExPASy.Enzyme
Bio.ExPASy.Prodoc
Bio.ExPASy.Prosite
Bio.ExPASy.ScanProsite
Bio.File
Bio.FSSP
Bio.FSSP.fssp_rec
Bio.FSSP.FSSPTools
Bio.GenBank
Bio.GenBank.Record
Bio.GenBank.Scanner
Bio.GenBank.utils
Bio.Geo
Bio.Geo.Record
Bio.Graphics
Bio.Graphics.BasicChromosome
Bio.Graphics.ColorSpiral
Bio.Graphics.Comparative
Bio.Graphics.DisplayRepresentation
Bio.Graphics.Distribution
Bio.Graphics.GenomeDiagram
Bio.Graphics.KGML_vis
Bio.HMM
Bio.HMM.DynamicProgramming
Bio.HMM.MarkovModel
Bio.HMM.Trainer
Bio.HMM.Utilities
Bio.KEGG
Bio.KEGG.Compound
Bio.KEGG.Enzyme
Bio.KEGG.Gene
Bio.KEGG.KGML
Bio.KEGG.KGML.KGML_parser
Bio.KEGG.KGML.KGML_pathway
Bio.KEGG.Map
Bio.KEGG.REST
Bio.kNN
Bio.LogisticRegression
Bio.MarkovModel
Bio.MaxEntropy
Bio.Medline
Bio.motifs
Bio.motifs.alignace
Bio.motifs.applications
Bio.motifs.clusterbuster
Bio.motifs.jaspar
Bio.motifs.jaspar.db
Bio.motifs.mast
Bio.motifs.matrix
Bio.motifs.meme
Bio.motifs.minimal
Bio.motifs.pfm
Bio.motifs.thresholds
Bio.motifs.transfac
Bio.motifs.xms
Bio.NaiveBayes
Bio.Nexus
Bio.Nexus.Nexus
Bio.Nexus.Nodes
Bio.Nexus.StandardData
Bio.Nexus.Trees
Bio.NMR
Bio.NMR.NOEtools
Bio.NMR.xpktools
Bio.pairwise2
Bio.Pathway
Bio.Pathway.Rep
Bio.Pathway.Rep.Graph
Bio.Pathway.Rep.MultiGraph
Bio.PDB
Bio.PDB.AbstractPropertyMap
Bio.PDB.Atom
Bio.PDB.Chain
Bio.PDB.Dice
Bio.PDB.DSSP
Bio.PDB.Entity
Bio.PDB.FragmentMapper
Bio.PDB.HSExposure
Bio.PDB.ic_data
Bio.PDB.ic_rebuild
Bio.PDB.internal_coords
Bio.PDB.MMCIF2Dict
Bio.PDB.mmcifio
Bio.PDB.MMCIFParser
Bio.PDB.mmtf
Bio.PDB.mmtf.DefaultParser
Bio.PDB.mmtf.mmtfio
Bio.PDB.Model
Bio.PDB.NACCESS
Bio.PDB.NeighborSearch
Bio.PDB.parse_pdb_header
Bio.PDB.PDBExceptions
Bio.PDB.PDBIO
Bio.PDB.PDBList
Bio.PDB.PDBParser
Bio.PDB.PICIO
Bio.PDB.Polypeptide
Bio.PDB.PSEA
Bio.PDB.QCPSuperimposer
Bio.PDB.Residue
Bio.PDB.ResidueDepth
Bio.PDB.SCADIO
Bio.PDB.Selection
Bio.PDB.Structure
Bio.PDB.StructureAlignment
Bio.PDB.StructureBuilder
Bio.PDB.Superimposer
Bio.PDB.vectors
Bio.phenotype
Bio.phenotype.phen_micro
Bio.phenotype.pm_fitting
Bio.Phylo
Bio.Phylo.Applications
Bio.Phylo.BaseTree
Bio.Phylo.CDAO
Bio.Phylo.CDAOIO
Bio.Phylo.Consensus
Bio.Phylo.Newick
Bio.Phylo.NewickIO
Bio.Phylo.NeXML
Bio.Phylo.NeXMLIO
Bio.Phylo.NexusIO
Bio.Phylo.PAML
Bio.Phylo.PAML.baseml
Bio.Phylo.PAML.chi2
Bio.Phylo.PAML.codeml
Bio.Phylo.PAML.yn00
Bio.Phylo.PhyloXML
Bio.Phylo.PhyloXMLIO
Bio.Phylo.TreeConstruction
Bio.PopGen
Bio.PopGen.GenePop
Bio.PopGen.GenePop.Controller
Bio.PopGen.GenePop.EasyController
Bio.PopGen.GenePop.FileParser
Bio.PopGen.GenePop.LargeFileParser
Bio.Restriction
Bio.Restriction.PrintFormat
Bio.Restriction.Restriction
Bio.Restriction.Restriction_Dictionary
Bio.SCOP
Bio.SCOP.Cla
Bio.SCOP.Des
Bio.SCOP.Dom
Bio.SCOP.Hie
Bio.SCOP.Raf
Bio.SCOP.Residues
Bio.SearchIO
Bio.SearchIO.BlastIO
Bio.SearchIO.BlastIO.blast_tab
Bio.SearchIO.BlastIO.blast_text
Bio.SearchIO.BlastIO.blast_xml
Bio.SearchIO.BlatIO
Bio.SearchIO.ExonerateIO
Bio.SearchIO.ExonerateIO.exonerate_cigar
Bio.SearchIO.ExonerateIO.exonerate_text
Bio.SearchIO.ExonerateIO.exonerate_vulgar
Bio.SearchIO.FastaIO
Bio.SearchIO.HHsuiteIO
Bio.SearchIO.HHsuiteIO.hhsuite2_text
Bio.SearchIO.HmmerIO
Bio.SearchIO.HmmerIO.hmmer2_text
Bio.SearchIO.HmmerIO.hmmer3_domtab
Bio.SearchIO.HmmerIO.hmmer3_tab
Bio.SearchIO.HmmerIO.hmmer3_text
Bio.SearchIO.InterproscanIO
Bio.SearchIO.InterproscanIO.interproscan_xml
Bio.Seq
Bio.SeqFeature
Bio.SeqIO
Bio.SeqIO.AbiIO
Bio.SeqIO.AceIO
Bio.SeqIO.FastaIO
Bio.SeqIO.GckIO
Bio.SeqIO.IgIO
Bio.SeqIO.InsdcIO
Bio.SeqIO.Interfaces
Bio.SeqIO.NibIO
Bio.SeqIO.PdbIO
Bio.SeqIO.PhdIO
Bio.SeqIO.PirIO
Bio.SeqIO.QualityIO
Bio.SeqIO.SeqXmlIO
Bio.SeqIO.SffIO
Bio.SeqIO.SnapGeneIO
Bio.SeqIO.SwissIO
Bio.SeqIO.TabIO
Bio.SeqIO.UniprotIO
Bio.SeqIO.XdnaIO
Bio.SeqRecord
Bio.Sequencing
Bio.Sequencing.Ace
Bio.Sequencing.Applications
Bio.Sequencing.Phd
Bio.SeqUtils
Bio.SeqUtils.CheckSum
Bio.SeqUtils.CodonUsage
Bio.SeqUtils.CodonUsageIndices
Bio.SeqUtils.IsoelectricPoint
Bio.SeqUtils.lcc
Bio.SeqUtils.MeltingTemp
Bio.SeqUtils.ProtParam
Bio.SeqUtils.ProtParamData
Bio.Statistics
Bio.Statistics.lowess
Bio.SubsMat
Bio.SubsMat.FreqTable
Bio.SubsMat.MatrixInfo
Bio.SVDSuperimposer
Bio.SwissProt
Bio.SwissProt.KeyWList
Bio.TogoWS
Bio.UniGene
Bio.UniProt
Bio.UniProt.GOA
Bio.Wise
Bio.Wise.dnal
Bio.Wise.psw
BioSQL
BioSQL.BioSeq
BioSQL.BioSeqDatabase
BioSQL.DBUtils
BioSQL.Loader
mol_seq() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
molar_extinction_coefficient() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
molecular_weight() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
(in module Bio.SeqUtils)
MolSeq (class in Bio.Phylo.PhyloXML)
mot() (Bio.Align.Applications.DialignCommandline property)
Motif (class in Bio.motifs)
(class in Bio.motifs.jaspar)
(class in Bio.motifs.meme)
(class in Bio.motifs.transfac)
move_track() (Bio.Graphics.GenomeDiagram.Diagram method)
msa_master_idx() (Bio.Blast.Applications.NcbipsiblastCommandline property)
MSAProbsCommandline (class in Bio.Align.Applications)
msf() (Bio.Align.Applications.DialignCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
MsfIterator (class in Bio.AlignIO.MsfIO)
msfout() (Bio.Align.Applications.MuscleCommandline property)
mttranslate() (Bio.Align.Applications.PrankCommandline property)
mult_align() (in module Bio.FSSP.FSSPTools)
multi_rot_Y() (in module Bio.PDB.vectors)
multi_rot_Z() (in module Bio.PDB.vectors)
MultiGraph (class in Bio.Pathway.Rep.MultiGraph)
multiple() (Bio.Phylo.Applications.PhymlCommandline property)
multiple_value_keys (Bio.motifs.transfac.Motif attribute)
MultipleAlignment (class in Bio.Blast.Record)
MultipleSeqAlignment (class in Bio.Align)
MuscleCommandline (class in Bio.Align.Applications)
MutableSeq (class in Bio.Seq)
Mysql_dbutils (class in BioSQL.DBUtils)
MysqlConnectorAdaptor (class in BioSQL.BioSeqDatabase)
N
n() (Bio.Align.Applications.DialignCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
N() (Bio.Sequencing.Applications.BwaAlignCommandline property)
n() (Bio.Sequencing.Applications.BwaAlignCommandline property)
N() (Bio.Sequencing.Applications.BwaBwaswCommandline property)
(Bio.Sequencing.Applications.BwaSampeCommandline property)
n() (Bio.Sequencing.Applications.BwaSampeCommandline property)
(Bio.Sequencing.Applications.BwaSamseCommandline property)
(Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
(Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline property)
(Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline property)
n_rand_starts() (Bio.Phylo.Applications.PhymlCommandline property)
NACCESS (class in Bio.PDB.NACCESS)
NACCESS_atomic (class in Bio.PDB.NACCESS)
NaiveBayes (class in Bio.NaiveBayes)
name() (Bio.KEGG.KGML.KGML_pathway.Entry property)
(Bio.KEGG.KGML.KGML_pathway.Pathway property)
(Bio.KEGG.KGML.KGML_pathway.Reaction property)
(Bio.Phylo.Applications.RaxmlCommandline property)
(Bio.Phylo.PhyloXMLIO.Writer method)
name_filter() (in module Bio.FSSP.FSSPTools)
namelength() (Bio.Align.Applications.MafftCommandline property)
NameWidth (Bio.Restriction.PrintFormat.PrintFormat attribute)
ncategories() (Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
NcbiblastformatterCommandline (class in Bio.Blast.Applications)
NcbiblastnCommandline (class in Bio.Blast.Applications)
NcbiblastpCommandline (class in Bio.Blast.Applications)
NcbiblastxCommandline (class in Bio.Blast.Applications)
NCBICodonTable (class in Bio.Data.CodonTable)
NCBICodonTableDNA (class in Bio.Data.CodonTable)
NCBICodonTableRNA (class in Bio.Data.CodonTable)
NcbideltablastCommandline (class in Bio.Blast.Applications)
NcbimakeblastdbCommandline (class in Bio.Blast.Applications)
NcbipsiblastCommandline (class in Bio.Blast.Applications)
NcbirpsblastCommandline (class in Bio.Blast.Applications)
NcbirpstblastnCommandline (class in Bio.Blast.Applications)
NcbitblastnCommandline (class in Bio.Blast.Applications)
NcbitblastxCommandline (class in Bio.Blast.Applications)
nclasses() (Bio.Phylo.Applications.PhymlCommandline property)
NeedleallCommandline (class in Bio.Emboss.Applications)
NeedleCommandline (class in Bio.Emboss.Applications)
negative() (Bio.Align.Applications.ClustalwCommandline property)
negative_gilist() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
negative_seqidlist() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
NeighborSearch (class in Bio.PDB.NeighborSearch)
Network (class in Bio.Pathway)
new_clade() (Bio.Phylo.CDAOIO.Parser method)
(Bio.Phylo.NewickIO.Parser method)
new_database() (BioSQL.BioSeqDatabase.DBServer method)
new_graph() (Bio.Graphics.GenomeDiagram.GraphSet method)
new_label() (Bio.Phylo.NeXMLIO.Writer method)
new_set() (Bio.Graphics.GenomeDiagram.Track method)
new_track() (Bio.Graphics.GenomeDiagram.Diagram method)
NewickError
newtree() (Bio.Align.Applications.ClustalwCommandline property)
newtree1() (Bio.Align.Applications.ClustalwCommandline property)
newtree2() (Bio.Align.Applications.ClustalwCommandline property)
NeXMLError
next_nonwhitespace() (Bio.Nexus.Nexus.CharBuffer method)
next_until() (Bio.Nexus.Nexus.CharBuffer method)
next_word() (Bio.Nexus.Nexus.CharBuffer method)
Nexus (class in Bio.Nexus.Nexus)
NexusError
,
[1]
NexusIterator() (in module Bio.AlignIO.NexusIO)
NexusWriter (class in Bio.AlignIO.NexusIO)
NibIterator (class in Bio.SeqIO.NibIO)
NibWriter (class in Bio.SeqIO.NibIO)
nj() (Bio.Phylo.Applications.FastTreeCommandline property)
(Bio.Phylo.TreeConstruction.DistanceTreeConstructor method)
njumble() (Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
nni() (Bio.Phylo.Applications.FastTreeCommandline property)
NNITreeSearcher (class in Bio.Phylo.TreeConstruction)
no2nd() (Bio.Phylo.Applications.FastTreeCommandline property)
no_greedy() (Bio.Blast.Applications.NcbiblastnCommandline property)
noanchors() (Bio.Align.Applications.MuscleCommandline property)
nobrief() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
nocat() (Bio.Phylo.Applications.FastTreeCommandline property)
nocore() (Bio.Align.Applications.MuscleCommandline property)
Node (class in Bio.Cluster)
(class in Bio.Nexus.Nodes)
(class in Bio.SCOP)
node() (Bio.Nexus.Trees.Tree method)
node_id() (Bio.Phylo.PhyloXMLIO.Writer method)
NodeData (class in Bio.Nexus.Trees)
NodeException
nodes() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
nofft() (Bio.Align.Applications.MafftCommandline property)
nofuzzy_end() (Bio.SeqFeature.CompoundLocation property)
(Bio.SeqFeature.FeatureLocation property)
nofuzzy_start() (Bio.SeqFeature.CompoundLocation property)
(Bio.SeqFeature.FeatureLocation property)
nohgap() (Bio.Align.Applications.ClustalwCommandline property)
nomatrix() (Bio.Phylo.Applications.FastTreeCommandline property)
nome() (Bio.Phylo.Applications.FastTreeCommandline property)
noml() (Bio.Phylo.Applications.FastTreeCommandline property)
NoneElement (class in Bio.Entrez.Parser)
nopgap() (Bio.Align.Applications.ClustalwCommandline property)
nopost() (Bio.Align.Applications.PrankCommandline property)
nopr() (Bio.Phylo.Applications.FastTreeCommandline property)
norm() (Bio.PDB.vectors.Vector method)
normalize() (Bio.motifs.matrix.FrequencyPositionMatrix method)
(Bio.PDB.vectors.Vector method)
normalize_letters() (in module Bio.SCOP.Raf)
normalized() (Bio.PDB.vectors.Vector method)
normsq() (Bio.PDB.vectors.Vector method)
noroot() (Bio.Emboss.Applications.FTreeDistCommandline property)
noscore() (Bio.Align.Applications.MafftCommandline property)
nosecstr1() (Bio.Align.Applications.ClustalwCommandline property)
nosecstr2() (Bio.Align.Applications.ClustalwCommandline property)
nosupport() (Bio.Phylo.Applications.FastTreeCommandline property)
notermini() (Bio.Emboss.Applications.IepCommandline property)
notop() (Bio.Phylo.Applications.FastTreeCommandline property)
notree() (Bio.Align.Applications.PrankCommandline property)
NotXMLError
NovoalignCommandline (class in Bio.Sequencing.Applications)
noweights() (Bio.Align.Applications.ClustalwCommandline property)
noxml() (Bio.Align.Applications.PrankCommandline property)
nt() (Bio.Align.Applications.DialignCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
nt_search() (in module Bio.SeqUtils)
nta() (Bio.Align.Applications.DialignCommandline property)
nuc() (Bio.Align.Applications.MafftCommandline property)
nucleotide_alphabet (Bio.Data.CodonTable.NCBICodonTable attribute)
(Bio.Data.CodonTable.NCBICodonTableDNA attribute)
(Bio.Data.CodonTable.NCBICodonTableRNA attribute)
num_alignments() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
num_bootstrap_searches() (Bio.Phylo.Applications.RaxmlCommandline property)
num_categories() (Bio.Phylo.Applications.RaxmlCommandline property)
num_descriptions() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
num_iterations() (Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
num_replicates() (Bio.Phylo.Applications.RaxmlCommandline property)
num_threads() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
number() (Bio.KEGG.KGML.KGML_pathway.Pathway property)
numiter() (Bio.Align.Applications.ClustalwCommandline property)
nummismatches() (Bio.Emboss.Applications.PalindromeCommandline property)
numreturn() (Bio.Emboss.Applications.Primer3Commandline property)
numthreads() (Bio.Align.Applications.MSAProbsCommandline property)
O
o() (Bio.Align.Applications.DialignCommandline property)
(Bio.Align.Applications.PrankCommandline property)
O() (Bio.Sequencing.Applications.BwaAlignCommandline property)
o() (Bio.Sequencing.Applications.BwaAlignCommandline property)
O() (Bio.Sequencing.Applications.BwaMemCommandline property)
o() (Bio.Sequencing.Applications.BwaSampeCommandline property)
(Bio.Sequencing.Applications.SamtoolsCatCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
(Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline property)
O() (Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline property)
o() (Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline property)
(Bio.Sequencing.Applications.SamtoolsViewCommandline property)
oanyself() (Bio.Emboss.Applications.Primer3Commandline property)
objscore() (Bio.Align.Applications.MuscleCommandline property)
observed_frequency_to_substitution_matrix() (in module Bio.SubsMat)
occ() (Bio.PDB.internal_coords.AtomKey.fieldsDef property)
odnaconc() (Bio.Emboss.Applications.Primer3Commandline property)
oendself() (Bio.Emboss.Applications.Primer3Commandline property)
oexcludedregion() (Bio.Emboss.Applications.Primer3Commandline property)
off_diagonal_range() (Bio.Blast.Applications.NcbiblastnCommandline property)
ogcmax() (Bio.Emboss.Applications.Primer3Commandline property)
ogcmin() (Bio.Emboss.Applications.Primer3Commandline property)
ogcopt() (Bio.Emboss.Applications.Primer3Commandline property)
ogcpercent() (Bio.Emboss.Applications.Primer3Commandline property)
ok_applies_to (Bio.Phylo.PhyloXML.Property attribute)
ok_datatype (Bio.Phylo.PhyloXML.Property attribute)
ok_rank (Bio.Phylo.PhyloXML.Taxonomy attribute)
ok_type (Bio.Phylo.PhyloXML.Events attribute)
(Bio.Phylo.PhyloXML.SequenceRelation attribute)
oligoinput() (Bio.Emboss.Applications.Primer3Commandline property)
omaxsize() (Bio.Emboss.Applications.Primer3Commandline property)
ominsize() (Bio.Emboss.Applications.Primer3Commandline property)
omishybmax() (Bio.Emboss.Applications.Primer3Commandline property)
once() (Bio.Align.Applications.PrankCommandline property)
one_to_index() (in module Bio.PDB.Polypeptide)
one_to_three() (in module Bio.PDB.Polypeptide)
OneOfPosition (class in Bio.SeqFeature)
op() (Bio.Align.Applications.MafftCommandline property)
open() (in module Bio.bgzf)
open_database() (in module BioSQL.BioSeqDatabase)
open_dtd_file() (Bio.Entrez.Parser.DataHandler method)
open_xsd_file() (Bio.Entrez.Parser.DataHandler method)
opolyxmax() (Bio.Emboss.Applications.Primer3Commandline property)
optimize() (Bio.Phylo.Applications.PhymlCommandline property)
options() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
opttm() (Bio.Emboss.Applications.Primer3Commandline property)
Organism (class in Bio.Graphics.BasicChromosome)
original_taxon_order() (Bio.Nexus.Nexus.Nexus property)
orthologs() (Bio.KEGG.KGML.KGML_pathway.Pathway property)
osaltconc() (Bio.Emboss.Applications.Primer3Commandline property)
osformat() (Bio.Emboss.Applications.SeqretCommandline property)
osize() (Bio.Emboss.Applications.Primer3Commandline property)
osizeopt() (Bio.Emboss.Applications.Primer3Commandline property)
Other (class in Bio.Phylo.PhyloXML)
other() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
OTHER_INTERNAL_FORMAT (Bio.GenBank.Record.Record attribute)
otm() (Bio.Emboss.Applications.Primer3Commandline property)
otmmax() (Bio.Emboss.Applications.Primer3Commandline property)
otmmin() (Bio.Emboss.Applications.Primer3Commandline property)
otmopt() (Bio.Emboss.Applications.Primer3Commandline property)
out() (Bio.Align.Applications.MuscleCommandline property)
(Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbimakeblastdbCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
out_ascii_pssm() (Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
out_block() (in module Bio.Geo.Record)
out_prefix() (Bio.Sequencing.Applications.SamtoolsVersion0xSortCommandline property)
out_pssm() (Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
outfile() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.MSAProbsCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
(Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
outfmt() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
outgrno() (Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
outgroup() (Bio.Phylo.Applications.RaxmlCommandline property)
outorder() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
output() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
(Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
output_file() (Bio.Sequencing.Applications.SamtoolsFixmateCommandline property)
(Bio.Sequencing.Applications.SamtoolsRmdupCommandline property)
outputorder() (Bio.Align.Applications.ClustalOmegaCommandline property)
OutputRecord (class in Bio.Emboss.PrimerSearch)
outputtree() (Bio.Align.Applications.ClustalwCommandline property)
outseq() (Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
outtreefile() (Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
overlap() (Bio.Emboss.Applications.PalindromeCommandline property)
ow() (Bio.Align.Applications.DialignCommandline property)
P
P() (Bio.Sequencing.Applications.BwaMemCommandline property)
p() (Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
PairedFastaQualIterator() (in module Bio.SeqIO.QualityIO)
pairgap() (Bio.Align.Applications.ClustalwCommandline property)
pairing() (Bio.Emboss.Applications.FTreeDistCommandline property)
pairs() (Bio.Align.Applications.ProbconsCommandline property)
PairwiseAligner (class in Bio.Align)
PairwiseAlignment (class in Bio.Align)
PairwiseAlignments (class in Bio.Align)
PalindromeCommandline (class in Bio.Emboss.Applications)
parameters (Bio.Application.AbstractCommandline attribute)
Parameters (class in Bio.Blast.Record)
paramfile() (Bio.Align.Applications.ProbconsCommandline property)
parent_edges() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
parents() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
pars() (Bio.Phylo.Applications.PhymlCommandline property)
parse() (Bio.Entrez.Parser.DataHandler method)
(Bio.GenBank.FeatureParser method)
(Bio.GenBank.RecordParser method)
(Bio.GenBank.Scanner.InsdcScanner method)
(Bio.KEGG.KGML.KGML_parser.KGMLParser method)
(Bio.Phylo.CDAOIO.Parser method)
(Bio.Phylo.NewickIO.Parser method)
(Bio.Phylo.NeXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.SeqIO.AbiIO.AbiIterator method)
(Bio.SeqIO.FastaIO.FastaIterator method)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)
(Bio.SeqIO.GckIO.GckIterator method)
(Bio.SeqIO.IgIO.IgIterator method)
(Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator method)
(Bio.SeqIO.InsdcIO.EmblIterator method)
(Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator method)
(Bio.SeqIO.InsdcIO.GenBankIterator method)
(Bio.SeqIO.InsdcIO.ImgtIterator method)
(Bio.SeqIO.Interfaces.SequenceIterator method)
(Bio.SeqIO.NibIO.NibIterator method)
(Bio.SeqIO.PdbIO.PdbSeqresIterator method)
(Bio.SeqIO.PirIO.PirIterator method)
(Bio.SeqIO.QualityIO.FastqPhredIterator method)
(Bio.SeqIO.QualityIO.QualPhredIterator method)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator method)
(Bio.SeqIO.SffIO.SffIterator method)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator method)
(Bio.SeqIO.TabIO.TabIterator method)
(Bio.SeqIO.UniprotIO.Parser method)
(Bio.SeqIO.XdnaIO.XdnaIterator method)
(in module Bio.AlignIO)
(in module Bio.Blast.NCBIXML)
(in module Bio.Compass)
(in module Bio.Emboss.Primer3)
(in module Bio.Entrez)
(in module Bio.ExPASy.cellosaurus)
(in module Bio.ExPASy.Enzyme)
(in module Bio.ExPASy.Prodoc)
(in module Bio.ExPASy.Prosite)
(in module Bio.GenBank)
(in module Bio.Geo)
(in module Bio.KEGG.Compound)
(in module Bio.KEGG.Enzyme)
(in module Bio.KEGG.Gene)
(in module Bio.KEGG.KGML.KGML_parser)
(in module Bio.KEGG.Map)
(in module Bio.Medline)
(in module Bio.motifs)
(in module Bio.phenotype)
(in module Bio.Phylo.CDAOIO)
(in module Bio.Phylo.NewickIO)
(in module Bio.Phylo.NeXMLIO)
(in module Bio.Phylo.NexusIO)
(in module Bio.Phylo.PhyloXMLIO)
(in module Bio.SCOP.Cla)
(in module Bio.SCOP.Des)
(in module Bio.SCOP.Dom)
(in module Bio.SCOP.Hie)
(in module Bio.SCOP.Raf)
(in module Bio.SearchIO)
(in module Bio.SeqIO)
(in module Bio.Sequencing.Ace)
(in module Bio.Sequencing.Phd)
(in module Bio.SwissProt)
(in module Bio.SwissProt.KeyWList)
(in module Bio.UniGene)
(in module Bio.Wise.psw)
parse_alignment_block() (Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser method)
(Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser method)
(Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser method)
parse_cds_features() (Bio.GenBank.Scanner.InsdcScanner method)
parse_children() (Bio.Phylo.CDAOIO.Parser method)
parse_deflines() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
parse_domain() (in module Bio.SCOP)
parse_feature() (Bio.GenBank.Scanner.InsdcScanner method)
parse_features() (Bio.GenBank.Scanner.InsdcScanner method)
parse_footer() (Bio.GenBank.Scanner.EmblScanner method)
(Bio.GenBank.Scanner.GenBankScanner method)
(Bio.GenBank.Scanner.InsdcScanner method)
parse_graph() (Bio.Phylo.CDAOIO.Parser method)
parse_handle_to_graph() (Bio.Phylo.CDAOIO.Parser method)
parse_header() (Bio.GenBank.Scanner.InsdcScanner method)
parse_hits() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
parse_hsp_alignments() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
parse_hsps() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
parse_key_value() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
parse_line() (in module Bio.Wise.psw)
parse_pdb_header() (in module Bio.PDB.parse_pdb_header)
parse_preamble() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
parse_qresult() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
parse_records() (Bio.GenBank.Scanner.InsdcScanner method)
parse_seqids() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
parse_xsd() (Bio.Entrez.Parser.DataHandler method)
Parser (class in Bio.ExPASy.ScanProsite)
(class in Bio.Phylo.CDAOIO)
(class in Bio.Phylo.NewickIO)
(class in Bio.Phylo.NeXMLIO)
(class in Bio.Phylo.PhyloXMLIO)
(class in Bio.SeqIO.UniprotIO)
ParserError
ParserFailureError
parsimony() (Bio.Phylo.Applications.RaxmlCommandline property)
parsimony_seed() (Bio.Phylo.Applications.RaxmlCommandline property)
ParsimonyScorer (class in Bio.Phylo.TreeConstruction)
ParsimonyTreeConstructor (class in Bio.Phylo.TreeConstruction)
partition_branch_lengths() (Bio.Phylo.Applications.RaxmlCommandline property)
partition_filename() (Bio.Phylo.Applications.RaxmlCommandline property)
parts() (Bio.SeqFeature.FeatureLocation property)
partsize() (Bio.Align.Applications.MafftCommandline property)
parttree() (Bio.Align.Applications.MafftCommandline property)
Pathway (class in Bio.KEGG.KGML.KGML_pathway)
pattern() (Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
pca() (in module Bio.Cluster)
pcb_vectors_pymol() (Bio.PDB.HSExposure.HSExposureCA method)
pdb() (Bio.FSSP.FSSPAlignDict method)
pdb_date() (in module Bio.PDB.PICIO)
PDB_REF (Bio.PDB.PDBList.PDBList attribute)
pdb_res_num (Bio.FSSP.fssp_rec.align attribute)
PdbAtomIterator() (in module Bio.SeqIO.PdbIO)
PDBConstructionException
PDBConstructionWarning
PDBException
PDBIO (class in Bio.PDB.PDBIO)
PDBList (class in Bio.PDB.PDBList)
PDBParser (class in Bio.PDB.PDBParser)
PdbSeqresIterator (class in Bio.SeqIO.PdbIO)
Peaklist (class in Bio.NMR.xpktools)
peek() (Bio.Nexus.Nexus.CharBuffer method)
peek_nonwhitespace() (Bio.Nexus.Nexus.CharBuffer method)
peek_word() (Bio.Nexus.Nexus.CharBuffer method)
penalty() (Bio.Blast.Applications.NcbiblastnCommandline property)
perc_identity() (Bio.Blast.Applications.NcbiblastnCommandline property)
percentid() (Bio.Align.Applications.ClustalOmegaCommandline property)
pfam_gc_mapping (Bio.AlignIO.StockholmIO.StockholmIterator attribute)
(Bio.AlignIO.StockholmIO.StockholmWriter attribute)
pfam_gr_mapping (Bio.AlignIO.StockholmIO.StockholmIterator attribute)
(Bio.AlignIO.StockholmIO.StockholmWriter attribute)
pfam_gs_mapping (Bio.AlignIO.StockholmIO.StockholmIterator attribute)
(Bio.AlignIO.StockholmIO.StockholmWriter attribute)
Pgdb_dbutils (class in BioSQL.DBUtils)
PhdIterator() (in module Bio.SeqIO.PhdIO)
PhdWriter (class in Bio.SeqIO.PhdIO)
phi_pattern() (Bio.Blast.Applications.NcbipsiblastCommandline property)
phred_quality_from_solexa() (in module Bio.SeqIO.QualityIO)
phyi() (Bio.Align.Applications.MuscleCommandline property)
phyiout() (Bio.Align.Applications.MuscleCommandline property)
PhylipIterator (class in Bio.AlignIO.PhylipIO)
phylipout() (Bio.Align.Applications.MafftCommandline property)
PhylipWriter (class in Bio.AlignIO.PhylipIO)
PhyloElement (class in Bio.Phylo.PhyloXML)
Phylogeny (class in Bio.Phylo.PhyloXML)
phylogeny() (Bio.Phylo.PhyloXMLIO.Writer method)
Phyloxml (class in Bio.Phylo.PhyloXML)
phyloxml() (Bio.Phylo.PhyloXMLIO.Writer method)
PhyloXMLError
PhyloXMLWarning
PhymlCommandline (class in Bio.Phylo.Applications)
phys() (Bio.Align.Applications.MuscleCommandline property)
physout() (Bio.Align.Applications.MuscleCommandline property)
pi() (Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint method)
pick_angle() (Bio.PDB.internal_coords.IC_Residue method)
pick_length() (Bio.PDB.internal_coords.IC_Residue method)
pim() (Bio.Align.Applications.ClustalwCommandline property)
PirIterator (class in Bio.SeqIO.PirIO)
PirWriter (class in Bio.SeqIO.PirIO)
PlateRecord (class in Bio.phenotype.phen_micro)
pmismatch() (Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
Point (class in Bio.Phylo.PhyloXML)
point() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
Polygon (class in Bio.Phylo.PhyloXML)
polygon() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
Polypeptide (class in Bio.PDB.Polypeptide)
pop() (Bio.Seq.MutableSeq method)
popitem() (Bio.Crystal.Crystal method)
pos_align_list2dict() (Bio.FSSP.FSSPAlignRec method)
pos_specific_score_matrix() (Bio.Align.AlignInfo.SummaryInfo method)
PosAlign (class in Bio.FSSP)
position() (Bio.SeqFeature.AfterPosition property)
(Bio.SeqFeature.BeforePosition property)
(Bio.SeqFeature.BetweenPosition property)
(Bio.SeqFeature.ExactPosition property)
(Bio.SeqFeature.OneOfPosition property)
(Bio.SeqFeature.UnknownPosition property)
(Bio.SeqFeature.WithinPosition property)
POSITION_PADDING (Bio.SeqIO.InsdcIO.EmblWriter attribute)
PositionGap (class in Bio.SeqFeature)
PositionSpecificScoringMatrix (class in Bio.motifs.matrix)
PositionWeightMatrix (class in Bio.motifs.matrix)
PPBuilder (class in Bio.PDB.Polypeptide)
prange() (Bio.Emboss.Applications.Primer3Commandline property)
PrankCommandline (class in Bio.Align.Applications)
pre() (Bio.Align.Applications.ProbconsCommandline property)
predictNOE() (in module Bio.NMR.NOEtools)
prefix() (Bio.Sequencing.Applications.BwaIndexCommandline property)
prefixes (Bio.Phylo.CDAOIO.Writer attribute)
PrefWidth (Bio.Restriction.PrintFormat.PrintFormat attribute)
pretty_print_prediction() (in module Bio.HMM.Utilities)
pretty_str() (Bio.PDB.internal_coords.IC_Residue method)
Primer3Commandline (class in Bio.Emboss.Applications)
Primers (class in Bio.Emboss.Primer3)
PrimerSearchCommandline (class in Bio.Emboss.Applications)
print_as() (Bio.Restriction.PrintFormat.PrintFormat method)
print_full_mat() (Bio.SubsMat.SeqMat method)
print_index() (Bio.SeqUtils.CodonUsage.CodonAdaptationIndex method)
print_info_content() (in module Bio.Align.AlignInfo)
print_mat() (Bio.SubsMat.SeqMat method)
print_matrix() (in module Bio.pairwise2)
print_options() (Bio.Phylo.PAML.codeml.Codeml method)
print_site_lnl() (Bio.Phylo.Applications.PhymlCommandline property)
print_that() (Bio.Restriction.PrintFormat.PrintFormat method)
print_trace() (Bio.Phylo.Applications.PhymlCommandline property)
PrintFormat (class in Bio.Restriction.PrintFormat)
printnodes() (Bio.Align.Applications.PrankCommandline property)
ProbconsCommandline (class in Bio.Align.Applications)
process_asa_data() (in module Bio.PDB.NACCESS)
process_clade() (Bio.Phylo.CDAOIO.Writer method)
(Bio.Phylo.NewickIO.Parser method)
process_rsa_data() (in module Bio.PDB.NACCESS)
products() (Bio.KEGG.KGML.KGML_pathway.Reaction property)
profile() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
profile1() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.ClustalwCommandline property)
profile2() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.ClustalwCommandline property)
progress() (Bio.Emboss.Applications.FNeighborCommandline property)
prop_invar() (Bio.Phylo.Applications.PhymlCommandline property)
Property (class in Bio.Phylo.PhyloXML)
property() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
protein_alphabet (Bio.Data.CodonTable.NCBICodonTable attribute)
protein_model() (Bio.Phylo.Applications.RaxmlCommandline property)
protein_models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute)
protein_scale() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
ProteinAnalysis (class in Bio.SeqUtils.ProtParam)
ProteinDomain (class in Bio.Phylo.PhyloXML)
ProtsimLine (class in Bio.UniGene)
prune() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
PSEA (class in Bio.PDB.PSEA)
psea() (in module Bio.PDB.PSEA)
psea2HEC() (in module Bio.PDB.PSEA)
pseudo() (Bio.Phylo.Applications.FastTreeCommandline property)
pseudocount() (Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
pseudocounts() (Bio.motifs.Motif property)
PSIBlast (class in Bio.Blast.Record)
psizeopt() (Bio.Emboss.Applications.Primer3Commandline property)
PSSM (class in Bio.Align.AlignInfo)
pssm() (Bio.motifs.Motif property)
pst() (Bio.Align.Applications.DialignCommandline property)
Psycopg2_dbutils (class in BioSQL.DBUtils)
ptmmax() (Bio.Emboss.Applications.Primer3Commandline property)
ptmmin() (Bio.Emboss.Applications.Primer3Commandline property)
ptmopt() (Bio.Emboss.Applications.Primer3Commandline property)
push_back() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
pwdist() (Bio.Align.Applications.PrankCommandline property)
pwdnamatrix() (Bio.Align.Applications.ClustalwCommandline property)
pwgapext() (Bio.Align.Applications.ClustalwCommandline property)
pwgapopen() (Bio.Align.Applications.ClustalwCommandline property)
pwgenomic() (Bio.Align.Applications.PrankCommandline property)
pwgenomicdist() (Bio.Align.Applications.PrankCommandline property)
pwm() (Bio.motifs.Motif property)
pwmatrix() (Bio.Align.Applications.ClustalwCommandline property)
Q
q() (Bio.Sequencing.Applications.BwaAlignCommandline property)
(Bio.Sequencing.Applications.BwaBwaswCommandline property)
Q() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
q() (Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
Q() (Bio.Sequencing.Applications.SamtoolsPhaseCommandline property)
q() (Bio.Sequencing.Applications.SamtoolsPhaseCommandline property)
Q() (Bio.Sequencing.Applications.SamtoolsTargetcutCommandline property)
q() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
qa (class in Bio.Sequencing.Ace)
qblast() (in module Bio.Blast.NCBIWWW)
qcov_hsp_perc() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
QCPSuperimposer (class in Bio.PDB.QCPSuperimposer)
qend_mark (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute)
qresult_end (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer attribute)
(Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer attribute)
qresult_start (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer attribute)
(Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer attribute)
qstart_mark (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute)
qual_digits() (Bio.Sequencing.Applications.NovoalignCommandline property)
Qualifier (class in Bio.GenBank.Record)
QUALIFIER_INDENT (Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
(Bio.SeqIO.InsdcIO.ImgtWriter attribute)
QUALIFIER_INDENT_STR (Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.ImgtWriter attribute)
QUALIFIER_INDENT_TMP (Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.ImgtWriter attribute)
quality() (Bio.Sequencing.Applications.NovoalignCommandline property)
QualPhredIterator (class in Bio.SeqIO.QualityIO)
QualPhredWriter (class in Bio.SeqIO.QualityIO)
quartiles() (Bio.Graphics.GenomeDiagram.GraphData method)
query() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
query_coverage() (Bio.Compass.Record method)
query_gencode() (Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
query_loc() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
quicktree() (Bio.Align.Applications.ClustalwCommandline property)
quiet() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.MafftCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
(Bio.Align.Applications.PrankCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
(Bio.Phylo.Applications.PhymlCommandline property)
quote() (Bio.Phylo.Applications.FastTreeCommandline property)
quotestrip() (in module Bio.Nexus.Nexus)
qUri() (in module Bio.Phylo.CDAOIO)
(in module Bio.Phylo.NeXMLIO)
R
R() (Bio.Sequencing.Applications.BwaAlignCommandline property)
r() (Bio.Sequencing.Applications.BwaBwaswCommandline property)
R() (Bio.Sequencing.Applications.BwaMemCommandline property)
r() (Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.BwaSampeCommandline property)
(Bio.Sequencing.Applications.BwaSamseCommandline property)
(Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
R() (Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
r() (Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
R() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
r() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
r_method() (Bio.Sequencing.Applications.NovoalignCommandline property)
r_seed() (Bio.Phylo.Applications.PhymlCommandline property)
rak() (Bio.PDB.internal_coords.IC_Residue method)
rand_start() (Bio.Phylo.Applications.PhymlCommandline property)
random_starting_tree() (Bio.Phylo.Applications.RaxmlCommandline property)
randomize() (Bio.Nexus.Trees.Tree method)
randomized() (Bio.Phylo.BaseTree.Tree class method)
range() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Graphics.GenomeDiagram.Diagram method)
(Bio.Graphics.GenomeDiagram.FeatureSet method)
(Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.Graphics.GenomeDiagram.GraphSet method)
(Bio.Graphics.GenomeDiagram.Track method)
rank() (Bio.Phylo.PhyloXMLIO.Writer method)
rapid_bootstrap_seed() (Bio.Phylo.Applications.RaxmlCommandline property)
rate() (Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
raw() (Bio.Nexus.StandardData.StandardData method)
rawdist() (Bio.Phylo.Applications.FastTreeCommandline property)
RaxmlCommandline (class in Bio.Phylo.Applications)
rd (class in Bio.Sequencing.Ace)
re_code (Bio.Phylo.PhyloXML.Taxonomy attribute)
re_doi (Bio.Phylo.PhyloXML.Reference attribute)
re_ref (Bio.Phylo.PhyloXML.Annotation attribute)
(Bio.Phylo.PhyloXML.Property attribute)
re_symbol (Bio.Phylo.PhyloXML.Sequence attribute)
re_value (Bio.Phylo.PhyloXML.MolSeq attribute)
reactant_ids() (Bio.KEGG.KGML.KGML_pathway.Reaction property)
Reaction (class in Bio.KEGG.KGML.KGML_pathway)
(class in Bio.Pathway)
reaction() (Bio.KEGG.KGML.KGML_pathway.Entry property)
reaction_entries() (Bio.KEGG.KGML.KGML_pathway.Pathway property)
reactions() (Bio.KEGG.KGML.KGML_pathway.Pathway property)
(Bio.Pathway.System method)
read() (Bio.bgzf.BgzfReader method)
(Bio.Entrez.Parser.DataHandler method)
(Bio.Nexus.Nexus.Nexus method)
(Bio.Phylo.PhyloXMLIO.Parser method)
(in module Bio.Affy.CelFile)
(in module Bio.Align.substitution_matrices)
(in module Bio.AlignIO)
(in module Bio.Blast.NCBIXML)
(in module Bio.Cluster)
(in module Bio.Compass)
(in module Bio.Emboss.Primer3)
(in module Bio.Emboss.PrimerSearch)
(in module Bio.Entrez)
(in module Bio.ExPASy.cellosaurus)
(in module Bio.ExPASy.Enzyme)
(in module Bio.ExPASy.Prodoc)
(in module Bio.ExPASy.Prosite)
(in module Bio.ExPASy.ScanProsite)
(in module Bio.GenBank)
(in module Bio.KEGG.Enzyme)
(in module Bio.KEGG.KGML.KGML_parser)
(in module Bio.Medline)
(in module Bio.motifs)
(in module Bio.motifs.alignace)
(in module Bio.motifs.clusterbuster)
(in module Bio.motifs.jaspar)
(in module Bio.motifs.mast)
(in module Bio.motifs.meme)
(in module Bio.motifs.minimal)
(in module Bio.motifs.pfm)
(in module Bio.motifs.transfac)
(in module Bio.motifs.xms)
(in module Bio.phenotype)
(in module Bio.Phylo.PAML.baseml)
(in module Bio.Phylo.PAML.codeml)
(in module Bio.Phylo.PAML.yn00)
(in module Bio.Phylo.PhyloXMLIO)
(in module Bio.PopGen.GenePop)
(in module Bio.PopGen.GenePop.FileParser)
(in module Bio.PopGen.GenePop.LargeFileParser)
(in module Bio.SearchIO)
(in module Bio.SeqIO)
(in module Bio.Sequencing.Ace)
(in module Bio.Sequencing.Phd)
(in module Bio.SwissProt)
(in module Bio.UniGene)
read_cal() (Bio.Sequencing.Applications.NovoalignCommandline property)
read_colorscheme() (Bio.Graphics.GenomeDiagram.ColorTranslator method)
read_count() (in module Bio.SubsMat.FreqTable)
read_ctl_file() (Bio.Phylo.PAML.baseml.Baseml method)
(Bio.Phylo.PAML.codeml.Codeml method)
(Bio.Phylo.PAML.yn00.Yn00 method)
read_file() (Bio.Sequencing.Applications.BwaAlignCommandline property)
(Bio.Sequencing.Applications.BwaBwaswCommandline property)
(Bio.Sequencing.Applications.BwaSamseCommandline property)
read_file1() (Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.BwaSampeCommandline property)
read_file2() (Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.BwaSampeCommandline property)
read_freq() (in module Bio.SubsMat.FreqTable)
read_fssp() (in module Bio.FSSP)
read_next() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
read_PIC() (in module Bio.PDB.PICIO)
read_text_matrix() (in module Bio.SubsMat)
read_v3() (in module Bio.Affy.CelFile)
read_v4() (in module Bio.Affy.CelFile)
reader_keywords (Bio.Blast.ParseBlastTable.BlastTableReader attribute)
readfile() (Bio.Sequencing.Applications.NovoalignCommandline property)
readline() (Bio.bgzf.BgzfReader method)
ReadRocheXmlManifest() (in module Bio.SeqIO.SffIO)
Reads (class in Bio.Sequencing.Ace)
realbranches() (Bio.Align.Applications.PrankCommandline property)
rearrange() (Bio.Emboss.Applications.FDNAParsCommandline property)
rearrangements() (Bio.Phylo.Applications.RaxmlCommandline property)
Record (class in Bio.Affy.CelFile)
(class in Bio.Cluster)
(class in Bio.Compass)
(class in Bio.Emboss.Primer3)
(class in Bio.ExPASy.cellosaurus)
(class in Bio.ExPASy.Enzyme)
(class in Bio.ExPASy.Prodoc)
(class in Bio.ExPASy.Prosite)
(class in Bio.ExPASy.ScanProsite)
(class in Bio.GenBank.Record)
(class in Bio.Geo.Record)
(class in Bio.KEGG.Compound)
(class in Bio.KEGG.Enzyme)
(class in Bio.KEGG.Gene)
(class in Bio.Medline)
(class in Bio.motifs.alignace)
(class in Bio.motifs.clusterbuster)
(class in Bio.motifs.jaspar)
(class in Bio.motifs.mast)
(class in Bio.motifs.meme)
(class in Bio.motifs.minimal)
(class in Bio.motifs.pfm)
(class in Bio.motifs.transfac)
(class in Bio.motifs.xms)
(class in Bio.PopGen.GenePop)
(class in Bio.PopGen.GenePop.LargeFileParser)
(class in Bio.SCOP.Cla)
(class in Bio.SCOP.Des)
(class in Bio.SCOP.Dom)
(class in Bio.SCOP.Hie)
(class in Bio.Sequencing.Phd)
(class in Bio.SwissProt)
(class in Bio.SwissProt.KeyWList)
(class in Bio.UniGene)
record_has() (in module Bio.UniProt.GOA)
RECORD_START (Bio.GenBank.Scanner.EmblScanner attribute)
(Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.GenBank.Scanner.InsdcScanner attribute)
recorded() (Bio.Sequencing.Applications.NovoalignCommandline property)
RecordParser (class in Bio.GenBank)
red() (Bio.Phylo.PhyloXMLIO.Writer method)
ref() (Bio.SeqFeature.CompoundLocation property)
(Bio.SeqFeature.SeqFeature property)
(Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
(Bio.Sequencing.Applications.SamtoolsFaidxCommandline property)
ref_db() (Bio.SeqFeature.CompoundLocation property)
(Bio.SeqFeature.SeqFeature property)
Reference (class in Bio.ExPASy.Prodoc)
(class in Bio.GenBank.Record)
(class in Bio.Phylo.PhyloXML)
(class in Bio.SeqFeature)
(class in Bio.SwissProt)
reference() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
(Bio.Sequencing.Applications.BwaAlignCommandline property)
(Bio.Sequencing.Applications.BwaBwaswCommandline property)
(Bio.Sequencing.Applications.BwaMemCommandline property)
(Bio.Sequencing.Applications.BwaSampeCommandline property)
(Bio.Sequencing.Applications.BwaSamseCommandline property)
reference_keys (Bio.motifs.transfac.Motif attribute)
refine() (Bio.Align.Applications.MuscleCommandline property)
refinew() (Bio.Align.Applications.MuscleCommandline property)
refinewindow() (Bio.Align.Applications.MuscleCommandline property)
refmat() (in module Bio.PDB.vectors)
refresh() (Bio.Phylo.Applications.FastTreeCommandline property)
region() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
register_ncbi_table() (in module Bio.Data.CodonTable)
regular() (Bio.Emboss.Applications.FSeqBootCommandline property)
Relation (class in Bio.KEGG.KGML.KGML_pathway)
relations() (Bio.KEGG.KGML.KGML_pathway.Pathway property)
relative_atom_re (Bio.PDB.internal_coords.IC_Residue attribute)
RelaxedPhylipIterator (class in Bio.AlignIO.PhylipIO)
RelaxedPhylipWriter (class in Bio.AlignIO.PhylipIO)
remote() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
remove() (Bio.Crystal.Chain method)
(Bio.Seq.MutableSeq method)
(BioSQL.Loader.DatabaseRemover method)
remove_component() (Bio.KEGG.KGML.KGML_pathway.Entry method)
remove_database() (BioSQL.BioSeqDatabase.DBServer method)
remove_edge() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
remove_entry() (Bio.KEGG.KGML.KGML_pathway.Pathway method)
remove_graphics() (Bio.KEGG.KGML.KGML_pathway.Entry method)
remove_loci_by_name() (Bio.PopGen.GenePop.FileParser.FileRecord method)
remove_loci_by_position() (Bio.PopGen.GenePop.FileParser.FileRecord method)
remove_locus_by_name() (Bio.PopGen.GenePop.FileParser.FileRecord method)
(Bio.PopGen.GenePop.Record method)
remove_locus_by_position() (Bio.PopGen.GenePop.FileParser.FileRecord method)
(Bio.PopGen.GenePop.Record method)
remove_node() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
remove_population() (Bio.PopGen.GenePop.FileParser.FileRecord method)
(Bio.PopGen.GenePop.Record method)
remove_reaction() (Bio.KEGG.KGML.KGML_pathway.Pathway method)
(Bio.Pathway.System method)
remove_relation() (Bio.KEGG.KGML.KGML_pathway.Pathway method)
remove_succ() (Bio.Nexus.Nodes.Node method)
renumber_tracks() (Bio.Graphics.GenomeDiagram.Diagram method)
reorder() (Bio.Align.Applications.MafftCommandline property)
repeats() (Bio.Sequencing.Applications.NovoalignCommandline property)
replace_entry() (in module Bio.NMR.xpktools)
replacement_dictionary() (Bio.Align.AlignInfo.SummaryInfo method)
report() (Bio.Sequencing.Applications.NovoalignCommandline property)
report_IC() (in module Bio.PDB.ic_rebuild)
reps() (Bio.Emboss.Applications.FSeqBootCommandline property)
Res (class in Bio.SCOP.Raf)
res_name (Bio.FSSP.fssp_rec.align attribute)
reset() (Bio.Blast.NCBIXML.BlastParser method)
Residue (class in Bio.PDB.Residue)
residue_depth() (in module Bio.PDB.ResidueDepth)
residue_dict() (Bio.NMR.xpktools.Peaklist method)
ResidueDepth (class in Bio.PDB.ResidueDepth)
residuenumber() (Bio.Align.Applications.ClustalOmegaCommandline property)
Residues (class in Bio.SCOP.Residues)
resname() (Bio.PDB.internal_coords.AtomKey.fieldsDef property)
respos() (Bio.PDB.internal_coords.AtomKey.fieldsDef property)
rest() (Bio.Nexus.Nexus.CharBuffer method)
retree() (Bio.Align.Applications.MafftCommandline property)
retrieve_pdb_file() (Bio.PDB.PDBList.PDBList method)
reverse() (Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Pathway.Reaction method)
(Bio.Seq.MutableSeq method)
reverse_complement() (Bio.motifs.Instances method)
(Bio.motifs.matrix.GenericPositionMatrix method)
(Bio.motifs.Motif method)
(Bio.Seq.MutableSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqRecord.SeqRecord method)
(in module Bio.Seq)
reverse_complement_rna() (Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
reverseinput() (Bio.Emboss.Applications.Primer3Commandline property)
reward() (Bio.Blast.Applications.NcbiblastnCommandline property)
rewriteformat() (Bio.Emboss.Applications.FSeqBootCommandline property)
rfind() (Bio.Seq.Seq method)
rformat() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
rho() (Bio.Align.Applications.PrankCommandline property)
richards() (in module Bio.phenotype.pm_fitting)
rid() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
right_multiply() (Bio.PDB.vectors.Vector method)
rindex() (Bio.Seq.Seq method)
rollback() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.DBServer method)
root() (Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Phylo.BaseTree.Clade property)
root1() (Bio.Align.Applications.MuscleCommandline property)
root2() (Bio.Align.Applications.MuscleCommandline property)
root_at_midpoint() (Bio.Phylo.BaseTree.Tree method)
root_with_outgroup() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.Tree method)
rotaxis() (in module Bio.PDB.vectors)
rotaxis2m() (in module Bio.PDB.vectors)
rotmat() (in module Bio.PDB.vectors)
Round (class in Bio.Blast.Record)
rpsdb() (Bio.Blast.Applications.NcbideltablastCommandline property)
rsplit() (Bio.Seq.Seq method)
rstrip() (Bio.Seq.Seq method)
rt (class in Bio.Sequencing.Ace)
run() (Bio.PDB.QCPSuperimposer.QCPSuperimposer method)
(Bio.Phylo.PAML.baseml.Baseml method)
(Bio.Phylo.PAML.codeml.Codeml method)
(Bio.Phylo.PAML.yn00.Yn00 method)
(Bio.SVDSuperimposer.SVDSuperimposer method)
run_id() (Bio.Phylo.Applications.PhymlCommandline property)
run_naccess() (in module Bio.PDB.NACCESS)
run_psea() (in module Bio.PDB.PSEA)
S
s() (Bio.Sequencing.Applications.BwaBwaswCommandline property)
S() (Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
(Bio.Sequencing.Applications.SamtoolsRmdupCommandline property)
s() (Bio.Sequencing.Applications.SamtoolsRmdupCommandline property)
S() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
safename() (in module Bio.Nexus.Nexus)
sai_file() (Bio.Sequencing.Applications.BwaSamseCommandline property)
sai_file1() (Bio.Sequencing.Applications.BwaSampeCommandline property)
sai_file2() (Bio.Sequencing.Applications.BwaSampeCommandline property)
salt_correction() (in module Bio.SeqUtils.MeltingTemp)
saltconc() (Bio.Emboss.Applications.Primer3Commandline property)
sam_file() (Bio.Sequencing.Applications.SamtoolsReheaderCommandline property)
SamtoolsCalmdCommandline (class in Bio.Sequencing.Applications)
SamtoolsCatCommandline (class in Bio.Sequencing.Applications)
SamtoolsFaidxCommandline (class in Bio.Sequencing.Applications)
SamtoolsFixmateCommandline (class in Bio.Sequencing.Applications)
SamtoolsIdxstatsCommandline (class in Bio.Sequencing.Applications)
SamtoolsIndexCommandline (class in Bio.Sequencing.Applications)
SamtoolsMergeCommandline (class in Bio.Sequencing.Applications)
SamtoolsMpileupCommandline (class in Bio.Sequencing.Applications)
SamtoolsPhaseCommandline (class in Bio.Sequencing.Applications)
SamtoolsReheaderCommandline (class in Bio.Sequencing.Applications)
SamtoolsRmdupCommandline (class in Bio.Sequencing.Applications)
SamtoolsSortCommandline (in module Bio.Sequencing.Applications)
SamtoolsTargetcutCommandline (class in Bio.Sequencing.Applications)
SamtoolsVersion0xSortCommandline (class in Bio.Sequencing.Applications)
SamtoolsVersion1xSortCommandline (class in Bio.Sequencing.Applications)
SamtoolsViewCommandline (class in Bio.Sequencing.Applications)
sanitize_name() (in module Bio.AlignIO.PhylipIO)
save() (Bio.Cluster.Record method)
(Bio.PDB.mmcifio.MMCIFIO method)
(Bio.PDB.mmtf.mmtfio.MMTFIO method)
(Bio.PDB.PDBIO.PDBIO method)
(in module Bio.MarkovModel)
save_dtd_file() (Bio.Entrez.Parser.DataHandler method)
save_each_pssm() (Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
save_pssm_after_last_round() (Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
save_xsd_file() (Bio.Entrez.Parser.DataHandler method)
scale_segment_value() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method)
scalebranches() (Bio.Align.Applications.PrankCommandline property)
ScaledDPAlgorithms (class in Bio.HMM.DynamicProgramming)
scan() (in module Bio.ExPASy.ScanProsite)
schemaHandler() (Bio.Entrez.Parser.DataHandler method)
scheme_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method)
scientific_name() (Bio.Phylo.PhyloXMLIO.Writer method)
Scop (class in Bio.SCOP)
score() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.PairwiseAligner method)
ScoreDistribution (class in Bio.motifs.thresholds)
scorefile() (Bio.Align.Applications.MuscleCommandline property)
Scorer (class in Bio.Phylo.TreeConstruction)
search() (Bio.AlignIO.MafIO.MafIndex method)
(Bio.motifs.Instances method)
(Bio.motifs.matrix.PositionSpecificScoringMatrix method)
(Bio.PDB.NeighborSearch.NeighborSearch method)
(Bio.Phylo.Applications.PhymlCommandline property)
(Bio.Phylo.TreeConstruction.NNITreeSearcher method)
(Bio.Phylo.TreeConstruction.TreeSearcher method)
(in module Bio.SCOP)
(in module Bio.TogoWS)
search_all() (Bio.PDB.NeighborSearch.NeighborSearch method)
search_count() (in module Bio.TogoWS)
search_iter() (in module Bio.TogoWS)
search_taxon() (Bio.Nexus.Trees.Tree method)
searchsp() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
second() (Bio.Phylo.Applications.FastTreeCommandline property)
secondary_structure_fraction() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
secstrout() (Bio.Align.Applications.ClustalwCommandline property)
seed() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.MafftCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Phylo.Applications.FastTreeCommandline property)
seek() (Bio.bgzf.BgzfReader method)
seek_position() (Bio.PopGen.GenePop.FileParser.FileRecord method)
seekable() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
seg() (Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
seguid() (in module Bio.SeqUtils.CheckSum)
Select (class in Bio.PDB.PDBIO)
select() (Bio.Align.substitution_matrices.Array method)
Seq (class in Bio.Seq)
seq() (Bio.SeqRecord.SeqRecord property)
(BioSQL.BioSeq.DBSeqRecord property)
seq1() (in module Bio.SeqUtils)
seq3() (in module Bio.SeqUtils)
SEQ_TYPES (Bio.Align.Applications.TCoffeeCommandline attribute)
seqall() (Bio.Emboss.Applications.PrimerSearchCommandline property)
SeqFeature (class in Bio.SeqFeature)
seqidlist() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
SeqMap (class in Bio.SCOP.Raf)
SeqMapIndex (class in Bio.SCOP.Raf)
SeqMat (class in Bio.SubsMat)
SeqmatchallCommandline (class in Bio.Emboss.Applications)
seqno_range() (Bio.Align.Applications.ClustalwCommandline property)
seqnos() (Bio.Align.Applications.ClustalwCommandline property)
SeqRecord (class in Bio.SeqRecord)
SeqretCommandline (class in Bio.Emboss.Applications)
seqtype() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
Sequence (class in Bio.Phylo.PhyloXML)
sequence() (Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.FSSP.FSSPAlignDict method)
(Bio.Phylo.PhyloXMLIO.Writer method)
SEQUENCE_FORMAT (Bio.GenBank.Record.Record attribute)
SEQUENCE_HEADERS (Bio.GenBank.Scanner.EmblScanner attribute)
(Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.GenBank.Scanner.InsdcScanner attribute)
SEQUENCE_INDENT (Bio.SeqIO.InsdcIO.GenBankWriter attribute)
sequence_relation() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
SequenceIterator (class in Bio.SeqIO.Interfaces)
SequenceLine (class in Bio.UniGene)
SequenceRelation (class in Bio.Phylo.PhyloXML)
sequences() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Phylo.Applications.RaxmlCommandline property)
SequenceWriter (class in Bio.SeqIO.Interfaces)
sequential() (Bio.Phylo.Applications.PhymlCommandline property)
SequentialAlignmentWriter (class in Bio.AlignIO.Interfaces)
SequentialPhylipIterator (class in Bio.AlignIO.PhylipIO)
SequentialPhylipWriter (class in Bio.AlignIO.PhylipIO)
SequentialSequenceWriter (class in Bio.SeqIO.Interfaces)
SeqXmlIterator (class in Bio.SeqIO.SeqXmlIO)
SeqXmlWriter (class in Bio.SeqIO.SeqXmlIO)
set() (Bio.Nexus.Nexus.StepMatrix method)
(Bio.PDB.QCPSuperimposer.QCPSuperimposer method)
(Bio.SVDSuperimposer.SVDSuperimposer method)
set_accuracy_95() (in module Bio.PDB.internal_coords)
set_all_features() (Bio.Graphics.GenomeDiagram.FeatureSet method)
set_all_tracks() (Bio.Graphics.GenomeDiagram.Diagram method)
set_altloc() (Bio.PDB.Atom.Atom method)
set_angle() (Bio.PDB.internal_coords.IC_Residue method)
set_anisou() (Bio.PDB.Atom.Atom method)
(Bio.PDB.StructureBuilder.StructureBuilder method)
set_atom_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_atoms() (Bio.PDB.Superimposer.Superimposer method)
set_bfactor() (Bio.PDB.Atom.Atom method)
set_bio_assembly_trans() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_cai_index() (Bio.SeqUtils.CodonUsage.CodonAdaptationIndex method)
set_chain_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_charge() (Bio.PDB.Atom.Atom method)
set_color() (Bio.Graphics.GenomeDiagram.Feature method)
set_colour() (Bio.Graphics.GenomeDiagram.Feature method)
set_coord() (Bio.PDB.Atom.Atom method)
set_data() (Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.Nexus.Nodes.Node method)
set_dict() (Bio.PDB.mmcifio.MMCIFIO method)
set_emission_pseudocount() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_emission_score() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_entity_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_equal_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_feature() (Bio.Graphics.GenomeDiagram.Feature method)
set_flexible() (Bio.PDB.internal_coords.IC_Residue method)
set_group_bond() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_group_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_handle() (Bio.GenBank.Scanner.InsdcScanner method)
set_hbond() (Bio.PDB.internal_coords.IC_Residue method)
set_header() (Bio.PDB.StructureBuilder.StructureBuilder method)
set_header_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_hedra() (Bio.PDB.internal_coords.Dihedron method)
set_hit_accession() (Bio.Blast.NCBIXML.BlastParser method)
set_hit_def() (Bio.Blast.NCBIXML.BlastParser method)
set_hit_id() (Bio.Blast.NCBIXML.BlastParser method)
set_hit_len() (Bio.Blast.NCBIXML.BlastParser method)
set_homog_trans_mtx() (in module Bio.PDB.vectors)
set_id() (Bio.Nexus.Nodes.Node method)
set_initial_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_inter_group_bond() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_length() (Bio.PDB.internal_coords.Hedron method)
(Bio.PDB.internal_coords.IC_Residue method)
set_line_counter() (Bio.PDB.StructureBuilder.StructureBuilder method)
set_model_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_occupancy() (Bio.PDB.Atom.Atom method)
set_original_taxon_order() (Bio.Nexus.Nexus.Nexus method)
set_parameter() (Bio.Application.AbstractCommandline method)
set_parent() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
set_prev() (Bio.Nexus.Nodes.Node method)
set_radius() (Bio.PDB.Atom.Atom method)
set_random_emission_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_random_initial_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_random_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_random_transition_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_residues() (Bio.PDB.internal_coords.IC_Chain method)
set_scale() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method)
set_serial_number() (Bio.PDB.Atom.Atom method)
set_sigatm() (Bio.PDB.Atom.Atom method)
(Bio.PDB.StructureBuilder.StructureBuilder method)
set_siguij() (Bio.PDB.Atom.Atom method)
(Bio.PDB.StructureBuilder.StructureBuilder method)
set_structure() (Bio.PDB.PDBIO.StructureIO method)
set_subtree() (Bio.Nexus.Trees.Tree method)
set_succ() (Bio.Nexus.Nodes.Node method)
set_symmetry() (Bio.PDB.StructureBuilder.StructureBuilder method)
set_transition_pseudocount() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_transition_score() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
set_X_homog_rot_mtx() (in module Bio.PDB.vectors)
set_xtal_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method)
set_Y_homog_rot_mtx() (in module Bio.PDB.vectors)
set_Z_homog_rot_mtx() (in module Bio.PDB.vectors)
setdefault() (Bio.Crystal.Crystal method)
SffIterator (class in Bio.SeqIO.SffIO)
SffWriter (class in Bio.SeqIO.SffIO)
sformat() (Bio.Emboss.Applications.SeqretCommandline property)
shortnames() (Bio.Align.Applications.PrankCommandline property)
show_domain_hits() (Bio.Blast.Applications.NcbideltablastCommandline property)
show_gis() (Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
showtree() (Bio.Align.Applications.PrankCommandline property)
showxml() (Bio.Align.Applications.PrankCommandline property)
shuffle() (Bio.Emboss.Applications.Est2GenomeCommandline property)
similarity() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
SimpleFastaParser() (in module Bio.SeqIO.FastaIO)
sink() (Bio.Pathway.Network method)
sink_interactions() (Bio.Pathway.Network method)
six_frame_translations() (in module Bio.SeqUtils)
sixmerpair() (Bio.Align.Applications.MafftCommandline property)
skip_header() (Bio.PopGen.GenePop.FileParser.FileRecord method)
skip_population() (Bio.PopGen.GenePop.FileParser.FileRecord method)
skip_whitespace() (Bio.Nexus.Nexus.CharBuffer method)
skipCharacterDataHandler() (Bio.Entrez.Parser.DataHandler method)
skipins() (Bio.Align.Applications.PrankCommandline property)
slow() (Bio.Phylo.Applications.FastTreeCommandline property)
slownni() (Bio.Phylo.Applications.FastTreeCommandline property)
smin() (Bio.Align.Applications.DialignCommandline property)
smoothscoreceil() (Bio.Align.Applications.MuscleCommandline property)
smoothwindow() (Bio.Align.Applications.MuscleCommandline property)
smprint() (Bio.Nexus.Nexus.StepMatrix method)
SnapGeneIterator (class in Bio.SeqIO.SnapGeneIO)
snucleotide() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
soft_masking() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
solexa_quality_from_phred() (in module Bio.SeqIO.QualityIO)
somcluster() (Bio.Cluster.Record method)
(in module Bio.Cluster)
sort() (Bio.Align.MultipleSeqAlignment method)
(Bio.Cluster.Tree method)
(Bio.PDB.Residue.DisorderedResidue method)
(Bio.PDB.Residue.Residue method)
(Bio.Sequencing.Ace.ACEFileRecord method)
source() (Bio.Pathway.Network method)
source_interactions() (Bio.Pathway.Network method)
sp() (Bio.Align.Applications.MuscleCommandline property)
space() (Bio.Emboss.Applications.Est2GenomeCommandline property)
SpacerSegment (class in Bio.Graphics.BasicChromosome)
speciations() (Bio.Phylo.PhyloXMLIO.Writer method)
species() (Bio.Pathway.Network method)
(Bio.Pathway.Reaction method)
(Bio.Pathway.System method)
splice() (Bio.Emboss.Applications.Est2GenomeCommandline property)
splicepenalty() (Bio.Emboss.Applications.Est2GenomeCommandline property)
split() (Bio.Nexus.Trees.Tree method)
(Bio.Phylo.BaseTree.TreeMixin method)
(Bio.Seq.Seq method)
split_in_loci() (Bio.PopGen.GenePop.Record method)
split_in_pops() (Bio.PopGen.GenePop.Record method)
split_jaspar_id() (in module Bio.motifs.jaspar)
split_virtual_offset() (in module Bio.bgzf)
spn() (Bio.Align.Applications.MuscleCommandline property)
spr() (Bio.Phylo.Applications.FastTreeCommandline property)
sprlength() (Bio.Phylo.Applications.FastTreeCommandline property)
sprotein() (Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
spscore() (Bio.Align.Applications.MuscleCommandline property)
Sqlite_dbutils (class in BioSQL.DBUtils)
ss1 (Bio.FSSP.fssp_rec.align attribute)
ss_to_index() (in module Bio.PDB.DSSP)
stable() (Bio.Align.Applications.MuscleCommandline property)
StandardData (class in Bio.Nexus.StandardData)
stars() (Bio.Align.Applications.DialignCommandline property)
start() (Bio.SeqFeature.CompoundLocation property)
(Bio.SeqFeature.FeatureLocation property)
start_aa_list (Bio.FSSP.fssp_rec.align attribute)
start_codons (Bio.Data.CodonTable.CodonTable attribute)
start_read() (Bio.PopGen.GenePop.FileParser.FileRecord method)
startA() (Bio.Graphics.GenomeDiagram.CrossLink property)
startB() (Bio.Graphics.GenomeDiagram.CrossLink property)
startDBRefElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
startDescriptionElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
startDocument() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
startElement() (Bio.ExPASy.ScanProsite.ContentHandler method)
startElementHandler() (Bio.Entrez.Parser.DataHandler method)
startEntryElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
startEntryFieldElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
starting_tree() (Bio.Phylo.Applications.RaxmlCommandline property)
startNamespaceDeclHandler() (Bio.Entrez.Parser.DataHandler method)
startPropertyElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
startRawElementHandler() (Bio.Entrez.Parser.DataHandler method)
startSequenceElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
startSeqXMLElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
startSkipElementHandler() (Bio.Entrez.Parser.DataHandler method)
startSpeciesElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
startswith() (Bio.Seq.Seq method)
Statistics (class in Bio.Wise.dnal)
stats() (Bio.Align.Applications.ClustalwCommandline property)
std() (Bio.motifs.matrix.PositionSpecificScoringMatrix method)
stdev() (Bio.Graphics.GenomeDiagram.GraphData method)
stdo() (Bio.Align.Applications.DialignCommandline property)
stdout() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
StepMatrix (class in Bio.Nexus.Nexus)
stochiometry() (Bio.Pathway.System method)
StockholmIterator (class in Bio.AlignIO.StockholmIO)
StockholmWriter (class in Bio.AlignIO.StockholmIO)
stop_codons (Bio.Data.CodonTable.CodonTable attribute)
store() (Bio.Entrez.Parser.DictionaryElement method)
(Bio.Entrez.Parser.ListElement method)
strand() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
(Bio.SeqFeature.CompoundLocation property)
(Bio.SeqFeature.FeatureLocation property)
(Bio.SeqFeature.SeqFeature property)
strandendin() (Bio.Align.Applications.ClustalwCommandline property)
strandendout() (Bio.Align.Applications.ClustalwCommandline property)
strandgap() (Bio.Align.Applications.ClustalwCommandline property)
StreamModeError
StretcherCommandline (class in Bio.Emboss.Applications)
strict_consensus() (in module Bio.Phylo.Consensus)
StringElement (class in Bio.Entrez.Parser)
strings (Bio.ExPASy.ScanProsite.ContentHandler attribute)
strip() (Bio.Seq.Seq method)
Structure (class in Bio.PDB.Structure)
structure_rebuild_test() (in module Bio.PDB.ic_rebuild)
StructureAlignment (class in Bio.PDB.StructureAlignment)
StructureBuilder (class in Bio.PDB.StructureBuilder)
STRUCTURED_COMMENT_DELIM (Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
STRUCTURED_COMMENT_END (Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
STRUCTURED_COMMENT_START (Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
StructureDecoder (class in Bio.PDB.mmtf.DefaultParser)
StructureIO (class in Bio.PDB.PDBIO)
STSLine (class in Bio.UniGene)
style() (Bio.Emboss.Applications.FTreeDistCommandline property)
subcomponent_size() (Bio.Graphics.BasicChromosome.Chromosome method)
subject() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
subject_loc() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
SubstitutionMatrix (class in Bio.SubsMat)
substitutions() (Bio.Align.MultipleSeqAlignment property)
substrates() (Bio.KEGG.KGML.KGML_pathway.Reaction property)
subtract_control() (Bio.phenotype.phen_micro.PlateRecord method)
sueff() (Bio.Align.Applications.MuscleCommandline property)
sum() (Bio.Nexus.Nexus.StepMatrix method)
(Bio.SubsMat.SeqMat method)
sum_branchlength() (Bio.Nexus.Trees.Tree method)
sum_statistics() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
sum_stats() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
SummaryInfo (class in Bio.Align.AlignInfo)
Superimposer (class in Bio.PDB.Superimposer)
sv() (Bio.Align.Applications.MuscleCommandline property)
SVDSuperimposer (class in Bio.SVDSuperimposer)
SwissIterator() (in module Bio.SeqIO.SwissIO)
SwissProtParserError
symbol() (Bio.Phylo.PhyloXMLIO.Writer method)
synonym() (Bio.Phylo.PhyloXMLIO.Writer method)
System (class in Bio.Pathway)
T
t() (Bio.Align.Applications.PrankCommandline property)
(Bio.Sequencing.Applications.BwaAlignCommandline property)
T() (Bio.Sequencing.Applications.BwaBwaswCommandline property)
t() (Bio.Sequencing.Applications.BwaBwaswCommandline property)
T() (Bio.Sequencing.Applications.BwaMemCommandline property)
t() (Bio.Sequencing.Applications.BwaMemCommandline property)
T() (Bio.Sequencing.Applications.SamtoolsVersion1xSortCommandline property)
t() (Bio.Sequencing.Applications.SamtoolsViewCommandline property)
ta() (Bio.Align.Applications.DialignCommandline property)
TabIterator (class in Bio.SeqIO.TabIO)
table() (Bio.Emboss.Applications.TranalignCommandline property)
TabWriter (class in Bio.SeqIO.TabIO)
target() (Bio.Emboss.Applications.Primer3Commandline property)
task() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
taxid() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
taxid_map() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
Taxonomy (class in Bio.Phylo.PhyloXML)
taxonomy() (Bio.Phylo.PhyloXML.Clade property)
(Bio.Phylo.PhyloXMLIO.Writer method)
TCoffeeCommandline (class in Bio.Align.Applications)
tell() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
TelomereSegment (class in Bio.Graphics.BasicChromosome)
template_length() (Bio.Blast.Applications.NcbiblastnCommandline property)
template_type() (Bio.Blast.Applications.NcbiblastnCommandline property)
termgap() (Bio.Align.Applications.PrankCommandline property)
terminal_gap_to_missing() (Bio.Nexus.Nexus.Nexus method)
terminalgap() (Bio.Align.Applications.ClustalwCommandline property)
test() (Bio.Emboss.Applications.FSeqBootCommandline property)
test_genic_diff_all() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_genic_diff_pair() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_genotypic_diff_all() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_genotypic_diff_pair() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_global_hz_deficiency() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_global_hz_excess() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_hw_global() (Bio.PopGen.GenePop.EasyController.EasyController method)
test_hw_pop() (Bio.PopGen.GenePop.EasyController.EasyController method)
test_ld() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_ld_all_pair() (Bio.PopGen.GenePop.EasyController.EasyController method)
test_pop_hz_deficiency() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_pop_hz_excess() (Bio.PopGen.GenePop.Controller.GenePopController method)
test_pop_hz_prob() (Bio.PopGen.GenePop.Controller.GenePopController method)
thorough() (Bio.Emboss.Applications.FDNAParsCommandline property)
thr() (Bio.Align.Applications.DialignCommandline property)
thread() (Bio.Align.Applications.MafftCommandline property)
threads() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Phylo.Applications.RaxmlCommandline property)
three_to_index() (in module Bio.PDB.Polypeptide)
three_to_one() (in module Bio.PDB.Polypeptide)
thresh() (Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
threshold() (Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Sequencing.Applications.NovoalignCommandline property)
threshold_balanced() (Bio.motifs.thresholds.ScoreDistribution method)
threshold_fnr() (Bio.motifs.thresholds.ScoreDistribution method)
threshold_fpr() (Bio.motifs.thresholds.ScoreDistribution method)
threshold_patser() (Bio.motifs.thresholds.ScoreDistribution method)
title() (Bio.Blast.Applications.NcbimakeblastdbCommandline property)
tm() (Bio.Align.Applications.MafftCommandline property)
Tm_GC() (in module Bio.SeqUtils.MeltingTemp)
Tm_NN() (in module Bio.SeqUtils.MeltingTemp)
Tm_staluc() (in module Bio.SeqUtils.MeltingTemp)
Tm_Wallace() (in module Bio.SeqUtils.MeltingTemp)
tname() (BioSQL.DBUtils.Generic_dbutils method)
to_alignment() (Bio.Phylo.PhyloXML.Phylogeny method)
to_dict() (Bio.motifs.jaspar.Record method)
(in module Bio.SearchIO)
(in module Bio.SeqIO)
to_generic() (Bio.Blast.Record.MultipleAlignment method)
to_hex() (Bio.Phylo.BaseTree.BranchColor method)
to_phylogeny() (Bio.Phylo.PhyloXML.Clade method)
to_phyloxml_container() (Bio.Phylo.PhyloXML.Phylogeny method)
to_rgb() (Bio.Phylo.BaseTree.BranchColor method)
to_seqfeature() (Bio.Phylo.PhyloXML.ProteinDomain method)
to_seqrecord() (Bio.Phylo.PhyloXML.Sequence method)
to_string() (Bio.Graphics.GenomeDiagram.FeatureSet method)
(Bio.Graphics.GenomeDiagram.GraphSet method)
(Bio.Graphics.GenomeDiagram.Track method)
(Bio.Nexus.Trees.Tree method)
to_strings() (Bio.Phylo.NewickIO.Writer method)
toClaRecord() (Bio.SCOP.Domain method)
toDesRecord() (Bio.SCOP.Domain method)
(Bio.SCOP.Node method)
toHieRecord() (Bio.SCOP.Node method)
toMultipleSeqAlignment() (Bio.codonalign.codonalignment.CodonAlignment method)
tomutable() (Bio.Seq.Seq method)
top() (Bio.Phylo.Applications.FastTreeCommandline property)
topdiags() (Bio.Align.Applications.ClustalwCommandline property)
topm() (Bio.Phylo.Applications.FastTreeCommandline property)
toSeq() (Bio.codonalign.codonseq.CodonSeq method)
toseq() (Bio.Seq.MutableSeq method)
(BioSQL.BioSeq.DBSeq method)
tossgaps() (Bio.Align.Applications.ClustalwCommandline property)
tostring() (Bio.Crystal.Crystal method)
(BioSQL.BioSeq.DBSeq method)
total_branch_length() (Bio.Phylo.BaseTree.TreeMixin method)
trace() (Bio.Nexus.Nodes.Chain method)
(Bio.Phylo.BaseTree.TreeMixin method)
Track (class in Bio.Graphics.GenomeDiagram)
train() (Bio.Align.Applications.ProbconsCommandline property)
(Bio.HMM.Trainer.BaumWelchTrainer method)
(Bio.HMM.Trainer.KnownStateTrainer method)
(in module Bio.kNN)
(in module Bio.LogisticRegression)
(in module Bio.MaxEntropy)
(in module Bio.NaiveBayes)
train_bw() (in module Bio.MarkovModel)
train_visible() (in module Bio.MarkovModel)
TrainingSequence (class in Bio.HMM.Trainer)
TranalignCommandline (class in Bio.Emboss.Applications)
transcribe() (Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(in module Bio.Seq)
transform() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Atom.DisorderedAtom method)
(Bio.PDB.Entity.Entity method)
transformation() (Bio.Nexus.Nexus.StepMatrix method)
transitions_from() (Bio.HMM.MarkovModel.HiddenMarkovModel method)
transitions_to() (Bio.HMM.MarkovModel.HiddenMarkovModel method)
translate() (Bio.Align.Applications.PrankCommandline property)
(Bio.codonalign.codonseq.CodonSeq method)
(Bio.Graphics.GenomeDiagram.ColorTranslator method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqRecord.SeqRecord method)
(in module Bio.Seq)
TranslationError
transpose() (Bio.Align.substitution_matrices.Array method)
transversion() (Bio.Emboss.Applications.FDNAParsCommandline property)
transweight() (Bio.Align.Applications.ClustalwCommandline property)
Tree (class in Bio.Cluster)
(class in Bio.Nexus.Trees)
(class in Bio.Phylo.BaseTree)
(class in Bio.Phylo.CDAO)
(class in Bio.Phylo.Newick)
(class in Bio.Phylo.NeXML)
tree() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.PrankCommandline property)
tree1() (Bio.Align.Applications.MuscleCommandline property)
tree2() (Bio.Align.Applications.MuscleCommandline property)
treecluster() (Bio.Cluster.Record method)
(in module Bio.Cluster)
TreeConstructor (class in Bio.Phylo.TreeConstruction)
TreeElement (class in Bio.Phylo.BaseTree)
TreeError
TreeMixin (class in Bio.Phylo.BaseTree)
treeout() (Bio.Align.Applications.MafftCommandline property)
treeprint() (Bio.Emboss.Applications.FNeighborCommandline property)
TreeSearcher (class in Bio.Phylo.TreeConstruction)
treetype() (Bio.Emboss.Applications.FNeighborCommandline property)
trimming() (Bio.Sequencing.Applications.NovoalignCommandline property)
trout() (Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
truncate() (Bio.Sequencing.Applications.NovoalignCommandline property)
ts_tv_ratio() (Bio.Phylo.Applications.PhymlCommandline property)
ttratio() (Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
turn3 (Bio.FSSP.fssp_rec.align attribute)
turn4 (Bio.FSSP.fssp_rec.align attribute)
turn5 (Bio.FSSP.fssp_rec.align attribute)
twice() (Bio.Align.Applications.PrankCommandline property)
two_mat_correlation() (in module Bio.SubsMat)
two_mat_DJS() (in module Bio.SubsMat)
two_mat_relative_entropy() (in module Bio.SubsMat)
type() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.TCoffeeCommandline property)
(Bio.Phylo.PhyloXMLIO.Writer method)
types (Bio.Phylo.PhyloXML.Sequence attribute)
U
U() (Bio.Sequencing.Applications.BwaMemCommandline property)
u() (Bio.Sequencing.Applications.SamtoolsCalmdCommandline property)
(Bio.Sequencing.Applications.SamtoolsMergeCommandline property)
(Bio.Sequencing.Applications.SamtoolsMpileupCommandline property)
(Bio.Sequencing.Applications.SamtoolsViewCommandline property)
UncertainPosition (class in Bio.SeqFeature)
unconverted() (Bio.Sequencing.Applications.NovoalignCommandline property)
UndoHandle (class in Bio.File)
unfold_entities() (in module Bio.PDB.Selection)
ungap() (Bio.codonalign.codonseq.CodonSeq method)
(Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
ungapped() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
uniform() (Bio.Emboss.Applications.ETandemCommandline property)
UniprotIterator() (in module Bio.SeqIO.UniprotIO)
uniqueify() (in module Bio.PDB.Selection)
UnknownPosition (class in Bio.SeqFeature)
UnknownSeq (class in Bio.Seq)
unlink() (Bio.Nexus.Nodes.Chain method)
unroot() (Bio.Nexus.Trees.Tree method)
update() (Bio.Align.substitution_matrices.Array method)
update_emissions() (Bio.HMM.Trainer.BaumWelchTrainer method)
update_pdb() (Bio.PDB.PDBList.PDBList method)
update_transitions() (Bio.HMM.Trainer.BaumWelchTrainer method)
upgma() (Bio.Phylo.TreeConstruction.DistanceTreeConstructor method)
upper() (Bio.Seq.Seq method)
(Bio.Seq.UnknownSeq method)
(Bio.SeqRecord.SeqRecord method)
Uri (class in Bio.Phylo.PhyloXML)
uri() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
use_index() (Bio.Blast.Applications.NcbiblastnCommandline property)
use_sw_tback() (Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
usekimura() (Bio.Align.Applications.ClustalOmegaCommandline property)
uselogs() (Bio.Align.Applications.PrankCommandline property)
usetree() (Bio.Align.Applications.ClustalwCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
usetree1() (Bio.Align.Applications.ClustalwCommandline property)
usetree2() (Bio.Align.Applications.ClustalwCommandline property)
V
v() (Bio.Sequencing.Applications.BwaMemCommandline property)
v_final() (Bio.Graphics.ColorSpiral.ColorSpiral property)
v_init() (Bio.Graphics.ColorSpiral.ColorSpiral property)
validate() (Bio.Crystal.Chain method)
validate_element() (Bio.Crystal.Chain method)
validate_key() (in module Bio.Crystal)
ValidationError
value() (Bio.Phylo.PhyloXMLIO.Writer method)
values() (Bio.Align.substitution_matrices.Array method)
(Bio.Crystal.Crystal method)
(Bio.Phylo.PhyloXML.Events method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
variation() (Bio.Sequencing.Applications.NovoalignCommandline property)
Vector (class in Bio.PDB.vectors)
vector_to_axis() (in module Bio.PDB.vectors)
verbose() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.MSAProbsCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
(Bio.Align.Applications.ProbconsCommandline property)
(Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
version() (Bio.Align.Applications.ClustalOmegaCommandline property)
(Bio.Align.Applications.MSAProbsCommandline property)
(Bio.Align.Applications.MuscleCommandline property)
(Bio.Blast.Applications.NcbiblastformatterCommandline property)
(Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbimakeblastdbCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
(Bio.motifs.jaspar.Motif property)
(Bio.Phylo.Applications.RaxmlCommandline property)
viterbi() (Bio.Align.Applications.ProbconsCommandline property)
(Bio.HMM.MarkovModel.HiddenMarkovModel method)
W
w() (Bio.Sequencing.Applications.BwaBwaswCommandline property)
(Bio.Sequencing.Applications.BwaMemCommandline property)
wa (class in Bio.Sequencing.Ace)
wag() (Bio.Phylo.Applications.FastTreeCommandline property)
warning() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.EInvertedCommandline property)
(Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.Emboss.Applications.ETandemCommandline property)
(Bio.Emboss.Applications.FConsenseCommandline property)
(Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FNeighborCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
(Bio.Emboss.Applications.FTreeDistCommandline property)
(Bio.Emboss.Applications.FuzznucCommandline property)
(Bio.Emboss.Applications.FuzzproCommandline property)
(Bio.Emboss.Applications.IepCommandline property)
(Bio.Emboss.Applications.NeedleallCommandline property)
(Bio.Emboss.Applications.NeedleCommandline property)
(Bio.Emboss.Applications.PalindromeCommandline property)
(Bio.Emboss.Applications.Primer3Commandline property)
(Bio.Emboss.Applications.PrimerSearchCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
(Bio.Emboss.Applications.SeqretCommandline property)
(Bio.Emboss.Applications.StretcherCommandline property)
(Bio.Emboss.Applications.TranalignCommandline property)
(Bio.Emboss.Applications.WaterCommandline property)
WaterCommandline (class in Bio.Emboss.Applications)
weblogo() (Bio.motifs.Motif method)
weight1() (Bio.Align.Applications.MuscleCommandline property)
weight2() (Bio.Align.Applications.MuscleCommandline property)
weight_filename() (Bio.Phylo.Applications.RaxmlCommandline property)
weighted_stepmatrix() (Bio.Nexus.Nexus.Nexus method)
weighti() (Bio.Align.Applications.MafftCommandline property)
weighting() (Bio.Nexus.Nexus.StepMatrix method)
weights() (Bio.Emboss.Applications.FDNADistCommandline property)
(Bio.Emboss.Applications.FDNAParsCommandline property)
(Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
(Bio.Emboss.Applications.FSeqBootCommandline property)
WellRecord (class in Bio.phenotype.phen_micro)
whichcode() (Bio.Emboss.Applications.FProtDistCommandline property)
(Bio.Emboss.Applications.FProtParsCommandline property)
width() (Bio.Emboss.Applications.Est2GenomeCommandline property)
(Bio.KEGG.KGML.KGML_pathway.Graphics property)
(Bio.Phylo.PhyloXMLIO.Writer method)
window() (Bio.Align.Applications.ClustalwCommandline property)
window_masker_db() (Bio.Blast.Applications.NcbiblastnCommandline property)
window_masker_taxid() (Bio.Blast.Applications.NcbiblastnCommandline property)
window_size() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
WithinPosition (class in Bio.SeqFeature)
word_size() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
wordsize() (Bio.Emboss.Applications.DiffseqCommandline property)
(Bio.Emboss.Applications.SeqmatchallCommandline property)
working_dir() (Bio.Phylo.Applications.RaxmlCommandline property)
wr (class in Bio.Sequencing.Ace)
wrap() (Bio.Align.Applications.ClustalOmegaCommandline property)
wrap_line() (in module Bio.Crystal)
write() (Bio.bgzf.BgzfWriter method)
(Bio.Graphics.GenomeDiagram.Diagram method)
(Bio.phenotype.phen_micro.JsonWriter method)
(Bio.Phylo.CDAOIO.Writer method)
(Bio.Phylo.NewickIO.Writer method)
(Bio.Phylo.NeXMLIO.Writer method)
(Bio.Phylo.PhyloXMLIO.Writer method)
(in module Bio.AlignIO)
(in module Bio.motifs)
(in module Bio.motifs.clusterbuster)
(in module Bio.motifs.jaspar)
(in module Bio.motifs.pfm)
(in module Bio.motifs.transfac)
(in module Bio.phenotype)
(in module Bio.Phylo.CDAOIO)
(in module Bio.Phylo.NewickIO)
(in module Bio.Phylo.NeXMLIO)
(in module Bio.Phylo.NexusIO)
(in module Bio.Phylo.PhyloXMLIO)
(in module Bio.SearchIO)
(in module Bio.SeqIO)
write_alignment() (Bio.AlignIO.ClustalIO.ClustalWriter method)
(Bio.AlignIO.Interfaces.SequentialAlignmentWriter method)
(Bio.AlignIO.MafIO.MafWriter method)
(Bio.AlignIO.MauveIO.MauveWriter method)
(Bio.AlignIO.NexusIO.NexusWriter method)
(Bio.AlignIO.PhylipIO.PhylipWriter method)
(Bio.AlignIO.PhylipIO.RelaxedPhylipWriter method)
(Bio.AlignIO.PhylipIO.SequentialPhylipWriter method)
(Bio.AlignIO.StockholmIO.StockholmWriter method)
write_cal() (Bio.Sequencing.Applications.NovoalignCommandline property)
write_cla() (Bio.SCOP.Scop method)
write_cla_sql() (Bio.SCOP.Scop method)
write_ctl_file() (Bio.Phylo.PAML.baseml.Baseml method)
(Bio.Phylo.PAML.codeml.Codeml method)
(Bio.Phylo.PAML.yn00.Yn00 method)
write_des() (Bio.SCOP.Scop method)
write_des_sql() (Bio.SCOP.Scop method)
write_file() (Bio.AlignIO.Interfaces.AlignmentWriter method)
(Bio.AlignIO.Interfaces.SequentialAlignmentWriter method)
(Bio.AlignIO.NexusIO.NexusWriter method)
(Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter method)
(Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter method)
(Bio.SearchIO.BlatIO.BlatPslWriter method)
(Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter method)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter method)
(Bio.SeqIO.Interfaces.SequenceWriter method)
(Bio.SeqIO.Interfaces.SequentialSequenceWriter method)
(Bio.SeqIO.NibIO.NibWriter method)
(Bio.SeqIO.SffIO.SffWriter method)
(Bio.SeqIO.XdnaIO.XdnaWriter method)
write_footer() (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method)
(Bio.SeqIO.Interfaces.SequenceWriter method)
(Bio.SeqIO.Interfaces.SequentialSequenceWriter method)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter method)
write_header() (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method)
(Bio.AlignIO.MafIO.MafWriter method)
(Bio.NMR.xpktools.Peaklist method)
(Bio.SeqIO.Interfaces.SequenceWriter method)
(Bio.SeqIO.Interfaces.SequentialSequenceWriter method)
(Bio.SeqIO.NibIO.NibWriter method)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter method)
(Bio.SeqIO.SffIO.SffWriter method)
write_hie() (Bio.SCOP.Scop method)
write_hie_sql() (Bio.SCOP.Scop method)
write_nexus_data() (Bio.Nexus.Nexus.Nexus method)
write_nexus_data_partitions() (Bio.Nexus.Nexus.Nexus method)
write_PDB() (in module Bio.PDB.ic_rebuild)
write_PIC() (Bio.PDB.internal_coords.IC_Residue method)
(in module Bio.PDB.PICIO)
write_record() (Bio.SeqIO.FastaIO.FastaWriter method)
(Bio.SeqIO.InsdcIO.EmblWriter method)
(Bio.SeqIO.InsdcIO.GenBankWriter method)
(Bio.SeqIO.Interfaces.SequenceWriter method)
(Bio.SeqIO.Interfaces.SequentialSequenceWriter method)
(Bio.SeqIO.NibIO.NibWriter method)
(Bio.SeqIO.PhdIO.PhdWriter method)
(Bio.SeqIO.PirIO.PirWriter method)
(Bio.SeqIO.QualityIO.FastqIlluminaWriter method)
(Bio.SeqIO.QualityIO.FastqPhredWriter method)
(Bio.SeqIO.QualityIO.FastqSolexaWriter method)
(Bio.SeqIO.QualityIO.QualPhredWriter method)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter method)
(Bio.SeqIO.SffIO.SffWriter method)
(Bio.SeqIO.TabIO.TabWriter method)
write_records() (Bio.SeqIO.Interfaces.SequenceWriter method)
(Bio.SeqIO.Interfaces.SequentialSequenceWriter method)
write_SCAD() (Bio.PDB.internal_coords.IC_Chain method)
(in module Bio.PDB.SCADIO)
write_to_string() (Bio.Graphics.GenomeDiagram.Diagram method)
writeanc() (Bio.Align.Applications.PrankCommandline property)
writebyproteinrec() (in module Bio.UniProt.GOA)
Writer (class in Bio.Phylo.CDAOIO)
(class in Bio.Phylo.NewickIO)
(class in Bio.Phylo.NeXMLIO)
(class in Bio.Phylo.PhyloXMLIO)
writerec() (in module Bio.UniProt.GOA)
writeToSQL() (Bio.SCOP.Astral method)
X
x() (Bio.KEGG.KGML.KGML_pathway.Graphics property)
XdnaIterator (class in Bio.SeqIO.XdnaIO)
XdnaWriter (class in Bio.SeqIO.XdnaIO)
xdrop_gap() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
xdrop_gap_final() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
xdrop_ungap() (Bio.Blast.Applications.NcbiblastnCommandline property)
(Bio.Blast.Applications.NcbiblastpCommandline property)
(Bio.Blast.Applications.NcbiblastxCommandline property)
(Bio.Blast.Applications.NcbideltablastCommandline property)
(Bio.Blast.Applications.NcbipsiblastCommandline property)
(Bio.Blast.Applications.NcbirpsblastCommandline property)
(Bio.Blast.Applications.NcbirpstblastnCommandline property)
(Bio.Blast.Applications.NcbitblastnCommandline property)
(Bio.Blast.Applications.NcbitblastxCommandline property)
xfr() (Bio.Align.Applications.DialignCommandline property)
xGC_skew() (in module Bio.SeqUtils)
xmlDeclHandler() (Bio.Entrez.Parser.DataHandler method)
XMSScanner (class in Bio.motifs.xms)
XpkEntry (class in Bio.NMR.xpktools)
Y
y() (Bio.KEGG.KGML.KGML_pathway.Graphics property)
Yn00 (class in Bio.Phylo.PAML.yn00)
Yn00Error
Z
z() (Bio.Sequencing.Applications.BwaBwaswCommandline property)
Biopython v: 1.78
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