Index

_

__abstractmethods__ (Bio.Align.a2m.AlignmentIterator attribute) (Bio.Align.a2m.AlignmentWriter attribute) (Bio.Align.bed.AlignmentIterator attribute) (Bio.Align.bed.AlignmentWriter attribute) (Bio.Align.bigbed.AlignmentIterator attribute) (Bio.Align.bigmaf.AlignmentIterator attribute) (Bio.Align.bigpsl.AlignmentIterator attribute) (Bio.Align.clustal.AlignmentIterator attribute) (Bio.Align.clustal.AlignmentWriter attribute) (Bio.Align.emboss.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentWriter attribute) (Bio.Align.fasta.AlignmentIterator attribute) (Bio.Align.fasta.AlignmentWriter attribute) (Bio.Align.hhr.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentWriter attribute) (Bio.Align.maf.AlignmentIterator attribute) (Bio.Align.maf.AlignmentWriter attribute) (Bio.Align.mauve.AlignmentIterator attribute) (Bio.Align.mauve.AlignmentWriter attribute) (Bio.Align.msf.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentWriter attribute) (Bio.Align.phylip.AlignmentIterator attribute) (Bio.Align.phylip.AlignmentWriter attribute) (Bio.Align.psl.AlignmentIterator attribute) (Bio.Align.psl.AlignmentWriter attribute) (Bio.Align.sam.AlignmentIterator attribute) (Bio.Align.sam.AlignmentWriter attribute) (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) (Bio.Align.tabular.AlignmentIterator attribute) (Bio.codonalign.codonseq.CodonSeq attribute) (Bio.motifs.meme.Instance attribute) (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.Seq.MutableSeq attribute) (Bio.Seq.Seq attribute) (Bio.Seq.SequenceDataAbstractBaseClass attribute) (Bio.SeqFeature.AfterPosition attribute) (Bio.SeqFeature.BeforePosition attribute) (Bio.SeqFeature.BetweenPosition attribute) (Bio.SeqFeature.CompoundLocation attribute) (Bio.SeqFeature.ExactPosition attribute) (Bio.SeqFeature.Location attribute) (Bio.SeqFeature.OneOfPosition attribute) (Bio.SeqFeature.Position attribute) (Bio.SeqFeature.SimpleLocation attribute) (Bio.SeqFeature.UncertainPosition attribute) (Bio.SeqFeature.UnknownPosition attribute) (Bio.SeqFeature.WithinPosition 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.TwoBitIO.TwoBitIterator attribute) (Bio.SeqIO.XdnaIO.XdnaIterator attribute) __add__() (Bio.Align.MultipleSeqAlignment method) (Bio.codonalign.codonalignment.CodonAlignment method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.SCOP.Raf.SeqMap method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.AfterPosition method) (Bio.SeqFeature.BeforePosition method) (Bio.SeqFeature.BetweenPosition method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.ExactPosition method) (Bio.SeqFeature.OneOfPosition method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqFeature.UnknownPosition method) (Bio.SeqFeature.WithinPosition method) (Bio.SeqRecord.SeqRecord method) __annotations__ (Bio.PDB.internal_coords.IC_Chain attribute) (Bio.PDB.internal_coords.IC_Residue attribute) __array__() (Bio.Align.Alignment method) __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) __bytes__() (Bio.Seq.SequenceDataAbstractBaseClass 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.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.internal_coords.Edron method) (Bio.PDB.internal_coords.IC_Residue method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.Phylo.PhyloXML.Events method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqRecord.SeqRecord method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __deepcopy__() (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.PDB.internal_coords.IC_Chain method) (Bio.PDB.internal_coords.IC_Residue method) __delitem__() (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) __enter__() (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) __eq__() (Bio.Align.Alignment 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.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.Reference method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqRecord.SeqRecord method) __exit__() (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) __format__() (Bio.Align.Alignment method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.substitution_matrices.Array method) (Bio.motifs.Motif method) (Bio.Phylo.BaseTree.Tree method) (Bio.SeqRecord.SeqRecord method) __ge__() (Bio.Align.Alignment 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.Seq.SequenceDataAbstractBaseClass 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.Alignment method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.PairwiseAlignments method) (Bio.Align.substitution_matrices.Array method) (Bio.codonalign.codonalignment.CodonAlignment method) (Bio.Data.CodonTable.AmbiguousForwardTable 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.SequenceDataAbstractBaseClass method) (Bio.SeqIO.TwoBitIO.TwoBitIterator method) (Bio.SeqRecord.SeqRecord method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __getnewargs__() (Bio.Align.AlignmentCounts method) (Bio.Align.bigbed.Field method) (Bio.pairwise2.Alignment method) (Bio.SeqFeature.BetweenPosition method) (Bio.SeqFeature.OneOfPosition method) (Bio.SeqFeature.WithinPosition method) __getstate__() (Bio.Align.PairwiseAligner method) __gt__() (Bio.Align.Alignment 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.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) __hash__ (Bio.Align.Alignment 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.SeqFeature.CompoundLocation attribute) (Bio.SeqFeature.Reference attribute) (Bio.SeqFeature.SeqFeature attribute) (Bio.SeqFeature.SimpleLocation 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.Seq.Seq method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.UnknownPosition method) __iadd__() (Bio.SCOP.Raf.SeqMap method) __init__() (Bio.Affy.CelFile.ParserError method) (Bio.Affy.CelFile.Record method) (Bio.Align.AlignInfo.PSSM method) (Bio.Align.AlignInfo.SummaryInfo method) (Bio.Align.Alignment 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.bed.AlignmentWriter method) (Bio.Align.bigbed.AutoSQLTable method) (Bio.Align.exonerate.AlignmentWriter method) (Bio.Align.interfaces.AlignmentIterator method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.mauve.AlignmentWriter method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.nexus.AlignmentWriter method) (Bio.Align.PairwiseAligner method) (Bio.Align.PairwiseAlignment method) (Bio.Align.PairwiseAlignments method) (Bio.Align.psl.AlignmentWriter method) (Bio.Align.sam.AlignmentWriter 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.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.DataHandlerMeta method) (Bio.Entrez.Parser.DictionaryElement method) (Bio.Entrez.Parser.ErrorElement method) (Bio.Entrez.Parser.IntegerElement method) (Bio.Entrez.Parser.ListElement method) (Bio.Entrez.Parser.NoneElement method) (Bio.Entrez.Parser.NotXMLError method) (Bio.Entrez.Parser.OrderedListElement method) (Bio.Entrez.Parser.StringElement 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.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.cealign.CEAligner 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.qcprot.QCPSuperimposer method) (Bio.PDB.QCPSuperimposer.QCPSuperimposer method) (Bio.PDB.Residue.DisorderedResidue method) (Bio.PDB.Residue.Residue method) (Bio.PDB.ResidueDepth.ResidueDepth method) (Bio.PDB.SASA.ShrakeRupley 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.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.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.PositionGap method) (Bio.SeqFeature.Reference method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation 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.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.TwoBitIO.TwoBitIterator 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.CodonAdaptationIndex method) (Bio.SeqUtils.CodonUsage.CodonAdaptationIndex method) (Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint method) (Bio.SeqUtils.ProtParam.ProteinAnalysis 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.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)

__iter__() (Bio.Align.interfaces.AlignmentIterator method) (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.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqIO.Interfaces.SequenceIterator method) (Bio.SeqRecord.SeqRecord method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __le__() (Bio.Align.Alignment 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.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) __len__() (Bio.Align.Alignment method) (Bio.Align.bigbed.AlignmentIterator method) (Bio.Align.hhr.AlignmentIterator method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.PairwiseAlignments method) (Bio.AlignIO.MafIO.MafIndex method) (Bio.Emboss.Primer3.Primers 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.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqIO.TwoBitIO.TwoBitIterator method) (Bio.SeqRecord.SeqRecord method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __lt__() (Bio.Align.Alignment 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.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) __mul__() (Bio.PDB.vectors.Vector method) (Bio.Seq.SequenceDataAbstractBaseClass method) __ne__() (Bio.Align.Alignment 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.SeqRecord.SeqRecord method) __neg__() (Bio.PDB.vectors.Vector method) __new__() (Bio.Align.AlignmentCounts static method) (Bio.Align.bigbed.Field static method) (Bio.Align.substitution_matrices.Array static method) (Bio.Entrez.Parser.ErrorElement static method) (Bio.Entrez.Parser.IntegerElement static method) (Bio.Entrez.Parser.StringElement static method) (Bio.pairwise2.Alignment static method) (Bio.Phylo.PhyloXML.Confidence 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.interfaces.AlignmentIterator method) (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.SimpleLocation method) __pow__() (Bio.PDB.vectors.Vector method) __radd__() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqRecord.SeqRecord method) __reduce__() (Bio.Align.substitution_matrices.Array method) __repr__() (Bio.Align.Alignment method) (Bio.Align.AlignmentCounts method) (Bio.Align.bigbed.Field method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.substitution_matrices.Array method) (Bio.AlignIO.MafIO.MafIndex method) (Bio.Application.AbstractCommandline method) (Bio.Application.ApplicationError method) (Bio.Data.CodonTable.NCBICodonTable method) (Bio.Entrez.Parser.DictionaryElement method) (Bio.Entrez.Parser.ErrorElement method) (Bio.Entrez.Parser.IntegerElement method) (Bio.Entrez.Parser.ListElement method) (Bio.Entrez.Parser.NoneElement method) (Bio.Entrez.Parser.OrderedListElement method) (Bio.Entrez.Parser.StringElement method) (Bio.ExPASy.cellosaurus.Record method) (Bio.ExPASy.Enzyme.Record method) (Bio.GenBank.Record.Feature method) (Bio.GenBank.Record.Qualifier method) (Bio.GenBank.utils.FeatureValueCleaner method) (Bio.pairwise2.Alignment 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.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.SeqFeature.AfterPosition method) (Bio.SeqFeature.BeforePosition method) (Bio.SeqFeature.BetweenPosition method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.ExactPosition method) (Bio.SeqFeature.Location method) (Bio.SeqFeature.OneOfPosition method) (Bio.SeqFeature.Position method) (Bio.SeqFeature.PositionGap method) (Bio.SeqFeature.Reference method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation 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) __setattr__() (Bio.Align.PairwiseAligner method) (Bio.Application.AbstractCommandline method) __setitem__() (Bio.Align.substitution_matrices.Array 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) __setstate__() (Bio.Align.PairwiseAligner method) (Bio.Align.substitution_matrices.Array method) __slots__ (Bio.Align.AlignmentCounts attribute) (Bio.Align.bigbed.Field attribute) (Bio.pairwise2.Alignment attribute) (Bio.Seq.SequenceDataAbstractBaseClass attribute) __str__() (Bio.Align.AlignInfo.PSSM method) (Bio.Align.Alignment method) (Bio.Align.bigbed.AutoSQLTable method) (Bio.Align.MultipleSeqAlignment 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.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.SeqFeature.AfterPosition method) (Bio.SeqFeature.BeforePosition method) (Bio.SeqFeature.BetweenPosition method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.ExactPosition method) (Bio.SeqFeature.OneOfPosition method) (Bio.SeqFeature.PositionGap method) (Bio.SeqFeature.Reference method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqFeature.WithinPosition method) (Bio.SeqRecord.SeqRecord method) (Bio.SeqUtils.CodonAdaptationIndex method) (Bio.SeqUtils.CodonUsage.CodonAdaptationIndex method) (Bio.Wise.dnal.Statistics 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.SeqFeature.SimpleLocation method) __truediv__() (Bio.PDB.vectors.Vector 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) AAsiz (Bio.PDB.internal_coords.IC_Chain attribute) AbiIterator (class in Bio.SeqIO.AbiIO) AbstractAtomPropertyMap (class in Bio.PDB.AbstractPropertyMap) AbstractCommandline (class in Bio.Application) AbstractDPAlgorithms (class in Bio.HMM.DynamicProgramming) AbstractPropertyMap (class in Bio.PDB.AbstractPropertyMap) AbstractResiduePropertyMap (class in Bio.PDB.AbstractPropertyMap) AbstractTrainer (class in Bio.HMM.Trainer) accept_atom() (Bio.PDB.Dice.ChainSelector method) (Bio.PDB.PDBIO.Select method) accept_atoms (Bio.PDB.internal_coords.IC_Residue attribute) accept_backbone (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) accept_sidechain (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_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.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 (Bio.Align.Applications.ClustalwCommandline property) (Bio.Emboss.Applications.Est2GenomeCommandline property) align() (Bio.Align.PairwiseAligner method) (Bio.PDB.cealign.CEAligner method) (in module Bio.Wise) (in module Bio.Wise.dnal) (in module Bio.Wise.psw) aligned (Bio.Align.Alignment property) alignment (Bio.Phylo.PhyloXML.Phylogeny property) Alignment (class in Bio.Align) (class in Bio.Blast.Record) (class in Bio.pairwise2) (class in Bio.Wise.psw) alignment_order (Bio.Align.Applications.MSAProbsCommandline property) AlignmentColumn (class in Bio.Wise.psw) AlignmentColumnFullException AlignmentCounts (class in Bio.Align) AlignmentHasDifferentLengthsError AlignmentIterator (class in Bio.Align.a2m) (class in Bio.Align.bed) (class in Bio.Align.bigbed) (class in Bio.Align.bigmaf) (class in Bio.Align.bigpsl) (class in Bio.Align.clustal) (class in Bio.Align.emboss) (class in Bio.Align.exonerate) (class in Bio.Align.fasta) (class in Bio.Align.hhr) (class in Bio.Align.interfaces) (class in Bio.Align.maf) (class in Bio.Align.mauve) (class in Bio.Align.msf) (class in Bio.Align.nexus) (class in Bio.Align.phylip) (class in Bio.Align.psl) (class in Bio.Align.sam) (class in Bio.Align.stockholm) (class in Bio.Align.tabular) (class in Bio.AlignIO.Interfaces)

AlignmentWriter (class in Bio.Align.a2m) (class in Bio.Align.bed) (class in Bio.Align.clustal) (class in Bio.Align.exonerate) (class in Bio.Align.fasta) (class in Bio.Align.interfaces) (class in Bio.Align.maf) (class in Bio.Align.mauve) (class in Bio.Align.nexus) (class in Bio.Align.phylip) (class in Bio.Align.psl) (class in Bio.Align.sam) (class in Bio.Align.stockholm) (class in Bio.AlignIO.Interfaces) all_ids() (Bio.Nexus.Nodes.Chain method) all_pairs() (in module Bio.Wise) 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_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) angle() (Bio.PDB.vectors.Vector method) angle_avg() (Bio.PDB.internal_coords.Dihedron static method) angle_dif() (Bio.PDB.internal_coords.Dihedron static method) angle_pop_sd() (Bio.PDB.internal_coords.Dihedron static 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.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.qcprot.QCPSuperimposer method) (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) assemble_residues_ser() (Bio.PDB.internal_coords.IC_Chain method) Astral (class in Bio.SCOP) atm() (Bio.PDB.internal_coords.AtomKey method) Atom (class in Bio.PDB.Atom) atom_chain (Bio.PDB.internal_coords.IC_Residue attribute) atom_re (Bio.PDB.internal_coords.AtomKey attribute) atom_sernum (Bio.PDB.internal_coords.IC_Residue attribute) atom_to_internal_coordinates() (Bio.PDB.Chain.Chain method) (Bio.PDB.internal_coords.IC_Chain method) (Bio.PDB.Model.Model method) (Bio.PDB.Structure.Structure method) atomArray (Bio.PDB.internal_coords.IC_Chain attribute) AtomIterator() (in module Bio.SeqIO.PdbIO) AtomKey (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) AutoSQLTable (class in Bio.Align.bigbed)

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() (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.a2m module Bio.Align.AlignInfo module Bio.Align.Applications module Bio.Align.bed module Bio.Align.bigbed module Bio.Align.bigmaf module Bio.Align.bigpsl module Bio.Align.clustal module Bio.Align.emboss module Bio.Align.exonerate module Bio.Align.fasta module Bio.Align.hhr module Bio.Align.interfaces module Bio.Align.maf module Bio.Align.mauve module Bio.Align.msf module Bio.Align.nexus module Bio.Align.phylip module Bio.Align.psl module Bio.Align.sam module Bio.Align.stockholm module Bio.Align.substitution_matrices module Bio.Align.tabular 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.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.codonalignment module Bio.codonalign.codonseq module Bio.Compass module Bio.Data module Bio.Data.CodonTable module Bio.Data.IUPACData module Bio.Data.PDBData 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.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.cealign 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.qcprot module Bio.PDB.QCPSuperimposer module Bio.PDB.Residue module Bio.PDB.ResidueDepth module Bio.PDB.SASA 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_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.TwoBitIO 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.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) bits() (Bio.PDB.internal_coords.Dihedron method) bl (Bio.Align.Applications.MafftCommandline property) Blast (class in Bio.Blast.Record) blastdb_version (Bio.Blast.Applications.NcbimakeblastdbCommandline property) 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) bond_rotate() (Bio.PDB.internal_coords.IC_Residue method) bond_set() (Bio.PDB.internal_coords.IC_Residue method) boot (Bio.Phylo.Applications.FastTreeCommandline property) bootlabels (Bio.Align.Applications.ClustalwCommandline property) bootstrap (Bio.Align.Applications.ClustalwCommandline property) (Bio.Phylo.Applications.PhymlCommandline property) bootstrap() (Bio.Nexus.Nexus.Nexus method) (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_atomArray() (Bio.PDB.internal_coords.IC_Chain method) build_edraArrays() (Bio.PDB.internal_coords.IC_Chain 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) (Bio.SeqUtils.CodonAdaptationIndex method) (in module Bio.kNN) (in module Bio.LogisticRegression) (in module Bio.MaxEntropy) (in module Bio.NaiveBayes) calculate_pseudocounts() (in module Bio.motifs.jaspar) 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) CEAligner (class in Bio.PDB.cealign) center (Bio.Align.Applications.MuscleCommandline property) center_of_mass() (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Entity.Entity method) centre (Bio.KEGG.KGML.KGML_pathway.Graphics property) Chain (class in Bio.Nexus.Nodes) (class in Bio.PDB.Chain) 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) Chromosome (class in Bio.Graphics.BasicChromosome) ChromosomeCounts (class in Bio.Graphics.DisplayRepresentation) ChromosomeSegment (class in Bio.Graphics.BasicChromosome) cic (Bio.PDB.internal_coords.Dihedron attribute) (Bio.PDB.internal_coords.Hedron attribute) CifAtomIterator() (in module Bio.SeqIO.PdbIO) CifSeqresIterator() (in module Bio.SeqIO.PdbIO) clade (Bio.Phylo.BaseTree.Tree property) 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.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_ic() (Bio.PDB.internal_coords.IC_Chain method) clear_transforms() (Bio.PDB.internal_coords.IC_Residue method) close (Bio.Phylo.Applications.FastTreeCommandline property) close() (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) (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) (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) color() (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) comment (Bio.Align.bigbed.Field attribute) 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) complement() (in module Bio.Seq) complement_rna() (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) compute() (Bio.PDB.SASA.ShrakeRupley method) confidence (Bio.Phylo.PhyloXML.Clade property) (Bio.Phylo.PhyloXML.Phylogeny property) Confidence (class in Bio.Phylo.PhyloXML) confidence() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) consensus (Bio.motifs.matrix.GenericPositionMatrix property) (Bio.motifs.Motif property) consensus() (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) convert() (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) copy() (Bio.Align.substitution_matrices.Array method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.vectors.Vector method) copy_initNCaCs() (Bio.PDB.internal_coords.IC_Chain method) core (Bio.Align.Applications.MuscleCommandline property) cores (Bio.Sequencing.Applications.NovoalignCommandline property) CorruptedXMLError count() (Bio.motifs.Instances method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) count_amino_acids() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) count_terminals() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) counts() (Bio.Align.Alignment method) cr_class() (Bio.PDB.internal_coords.AtomKey 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) 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_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) DataHandlerMeta (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) 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) dCoordSpace (Bio.PDB.internal_coords.IC_Chain attribute) dcsValid (Bio.PDB.internal_coords.IC_Chain attribute) 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) decode() (Bio.Seq.SequenceDataAbstractBaseClass method) DEFAULT_PSEUDO (Bio.HMM.MarkovModel.MarkovModelBuilder attribute) defined (Bio.Seq.SequenceDataAbstractBaseClass property) defined_ranges (Bio.Seq.SequenceDataAbstractBaseClass property) 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) difference() (Bio.PDB.internal_coords.Dihedron method) DifferentialCutsite (class in Bio.CAPS) DiffseqCommandline (class in Bio.Emboss.Applications) dihedral_signs() (Bio.PDB.internal_coords.IC_Chain method) Dihedron (class in Bio.PDB.internal_coords) dimer (Bio.Align.Applications.MuscleCommandline property) directory (Bio.Entrez.Parser.DataHandlerMeta 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_remove() (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Residue.DisorderedResidue 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) distance_plot() (Bio.PDB.internal_coords.IC_Chain method) distance_to_internal_coordinates() (Bio.PDB.internal_coords.IC_Chain method) 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) distplot_to_dh_arrays() (Bio.PDB.internal_coords.IC_Chain method) 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_all_assemblies() (Bio.PDB.PDBList.PDBList method) 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 (Bio.Align.Applications.DialignCommandline property) (class in Bio.Sequencing.Ace) 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) empty_status_characters (Bio.Align.maf.AlignmentIterator attribute) end (Bio.pairwise2.Alignment attribute) (Bio.SeqFeature.CompoundLocation property) (Bio.SeqFeature.SimpleLocation 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) 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.SequenceDataAbstractBaseClass 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 (Bio.KEGG.KGML.KGML_pathway.Reaction property) Entry (class in Bio.KEGG.KGML.KGML_pathway) entry() (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)

ErrorElement (class in Bio.Entrez.Parser) 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.BetweenPosition property) (Bio.SeqFeature.OneOfPosition property) (Bio.SeqFeature.Position property) (Bio.SeqFeature.WithinPosition property) externalEntityRefHandler() (Bio.Entrez.Parser.DataHandler method) extract() (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation 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) 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 (in module 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) fft (Bio.Align.Applications.MafftCommandline property) fgcolor (Bio.KEGG.KGML.KGML_pathway.Graphics property) Field (class in Bio.Align.bigbed) 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) 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) filtering_db (Bio.Blast.Applications.NcbiblastnCommandline property) finalize_structure() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) find() (Bio.Seq.SequenceDataAbstractBaseClass 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) 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 (Bio.Align.a2m.AlignmentIterator attribute) (Bio.Align.a2m.AlignmentWriter attribute) (Bio.Align.bed.AlignmentIterator attribute) (Bio.Align.bigbed.AlignmentIterator attribute) (Bio.Align.bigmaf.AlignmentIterator attribute) (Bio.Align.bigpsl.AlignmentIterator attribute) (Bio.Align.clustal.AlignmentIterator attribute) (Bio.Align.clustal.AlignmentWriter attribute) (Bio.Align.emboss.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentWriter attribute) (Bio.Align.fasta.AlignmentIterator attribute) (Bio.Align.fasta.AlignmentWriter attribute) (Bio.Align.hhr.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentWriter attribute) (Bio.Align.maf.AlignmentIterator attribute) (Bio.Align.maf.AlignmentWriter attribute) (Bio.Align.mauve.AlignmentIterator attribute) (Bio.Align.mauve.AlignmentWriter attribute) (Bio.Align.msf.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentWriter attribute) (Bio.Align.phylip.AlignmentIterator attribute) (Bio.Align.phylip.AlignmentWriter attribute) (Bio.Align.psl.AlignmentIterator attribute) (Bio.Align.psl.AlignmentWriter attribute) (Bio.Align.sam.AlignmentIterator attribute) (Bio.Align.sam.AlignmentWriter attribute) (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) (Bio.Align.tabular.AlignmentIterator attribute) 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.Sequencing.Applications.NovoalignCommandline property) format() (Bio.Align.Alignment method) (Bio.Align.substitution_matrices.Array method) (Bio.motifs.Motif method) (Bio.Phylo.BaseTree.Tree method) (Bio.SeqRecord.SeqRecord method) format_alignment() (Bio.Align.a2m.AlignmentWriter method) (Bio.Align.bed.AlignmentWriter method) (Bio.Align.clustal.AlignmentWriter method) (Bio.Align.fasta.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.maf.AlignmentWriter method) (Bio.Align.mauve.AlignmentWriter method) (Bio.Align.nexus.AlignmentWriter method) (Bio.Align.phylip.AlignmentWriter method) (Bio.Align.psl.AlignmentWriter method) (Bio.Align.sam.AlignmentWriter method) (Bio.Align.stockholm.AlignmentWriter method) (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 (Bio.Sequencing.Applications.NovoalignCommandline property) Fragment (class in Bio.PDB.FragmentMapper) 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) 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) fromstring() (Bio.SeqFeature.Location method) (Bio.SeqFeature.Position static method) (Bio.SeqFeature.SimpleLocation static method) FSeqBootCommandline (class in Bio.Emboss.Applications) fsm (Bio.Align.Applications.DialignCommandline property) 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) gaps (Bio.Align.AlignmentCounts attribute) 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_fraction() (in module Bio.SeqUtils) gc_mapping (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) 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_key() (Bio.PDB.internal_coords.Edron static method) gen_tuple() (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.Data.CodonTable.AmbiguousForwardTable method) get_acgt() (Bio.motifs.xms.XMSScanner method) get_alignment_length() (Bio.Align.MultipleSeqAlignment method) get_all_assemblies() (Bio.PDB.PDBList.PDBList method) get_all_entries() (Bio.PDB.PDBList.PDBList method) get_all_obsolete() (Bio.PDB.PDBList.PDBList 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_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_guide_coord_from_structure() (Bio.PDB.cealign.CEAligner 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.qcprot.QCPSuperimposer method) (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.qcprot.QCPSuperimposer method) (Bio.PDB.QCPSuperimposer.QCPSuperimposer method) (Bio.SVDSuperimposer.SVDSuperimposer method) get_rotran() (Bio.PDB.qcprot.QCPSuperimposer method) (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_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_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.qcprot.QCPSuperimposer method) (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) gf_mapping (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) 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) gr_mapping (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) 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) gs_mapping (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) 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_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)

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) 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) Id (class in Bio.Phylo.PhyloXML) id() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) id_width (Bio.AlignIO.PhylipIO.PhylipIterator attribute) identities (Bio.Align.AlignmentCounts 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.SCOP.Raf.SeqMap method) (Bio.Seq.SequenceDataAbstractBaseClass 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) indices (Bio.Align.Alignment property) infer_coordinates() (Bio.Align.Alignment class method) 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.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) inverse_indices (Bio.Align.Alignment 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.AtomKey method) (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_nucleic() (in module Bio.PDB.Polypeptide) 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) islower() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) isoelectric_point() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) IsoelectricPoint (class in Bio.SeqUtils.IsoelectricPoint) isprofile (Bio.Align.Applications.ClustalOmegaCommandline property) isupper() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) itemindex() (in module Bio.MarkovModel) items() (Bio.Align.substitution_matrices.Array 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) 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) key (Bio.Align.stockholm.AlignmentIterator attribute) keys() (Bio.Align.substitution_matrices.Array method) (Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method) (Bio.Phylo.PhyloXML.Events method) (Bio.SeqIO.TwoBitIO.TwoBitIterator method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method)

keys_to_process (Bio.GenBank.utils.FeatureValueCleaner attribute) keyword (Bio.Align.stockholm.AlignmentIterator 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) 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_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 (class in Bio.SeqFeature) 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) 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) lower() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) lstrip() (Bio.Seq.SequenceDataAbstractBaseClass 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_format() (Bio.Restriction.PrintFormat.PrintFormat method) make_table() (in module Bio.SeqUtils.MeltingTemp) make_virtual_offset() (in module Bio.bgzf) makematrix (Bio.Phylo.Applications.FastTreeCommandline property) map() (Bio.Align.Alignment method) 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.Align.tabular.State attribute) 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.Emboss.Applications.Primer3Commandline property) MaxSize (Bio.Restriction.PrintFormat.PrintFormat attribute) 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) mismatches (Bio.Align.AlignmentCounts attribute) 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.Align.bigbed.AlignmentIterator attribute) (Bio.Align.bigmaf.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentWriter attribute) (Bio.Emboss.Applications.Est2GenomeCommandline property) model (Bio.Phylo.Applications.PhymlCommandline property) (Bio.Phylo.Applications.RaxmlCommandline property) Model (class in Bio.PDB.Model) models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute) modify() (Bio.motifs.thresholds.ScoreDistribution method) module Bio Bio.Affy Bio.Affy.CelFile Bio.Align Bio.Align.a2m Bio.Align.AlignInfo Bio.Align.Applications Bio.Align.bed Bio.Align.bigbed Bio.Align.bigmaf Bio.Align.bigpsl Bio.Align.clustal Bio.Align.emboss Bio.Align.exonerate Bio.Align.fasta Bio.Align.hhr Bio.Align.interfaces Bio.Align.maf Bio.Align.mauve Bio.Align.msf Bio.Align.nexus Bio.Align.phylip Bio.Align.psl Bio.Align.sam Bio.Align.stockholm Bio.Align.substitution_matrices Bio.Align.tabular 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.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.codonalignment Bio.codonalign.codonseq Bio.Compass Bio.Data Bio.Data.CodonTable Bio.Data.IUPACData Bio.Data.PDBData 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.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.cealign 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.qcprot Bio.PDB.QCPSuperimposer Bio.PDB.Residue Bio.PDB.ResidueDepth Bio.PDB.SASA 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_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.TwoBitIO 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.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) multi_coord_space() (in module Bio.PDB.vectors) 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.Align.bigbed.Field attribute) (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) name() (Bio.Phylo.PhyloXMLIO.Writer method) 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) nj() (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_altloc (Bio.PDB.internal_coords.IC_Residue attribute) 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.SimpleLocation property) nofuzzy_start (Bio.SeqFeature.CompoundLocation property) (Bio.SeqFeature.SimpleLocation 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) NONE (Bio.Align.tabular.State attribute) 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) 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) OrderedListElement (class in Bio.Entrez.Parser) 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) ParallelAssembleResidues (Bio.PDB.internal_coords.IC_Chain attribute) 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.TwoBitIO.TwoBitIterator method) (Bio.SeqIO.UniprotIO.Parser method) (Bio.SeqIO.XdnaIO.XdnaIterator method) (in module Bio.Align) (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_btop() (Bio.Align.tabular.AlignmentIterator method) parse_cds_features() (Bio.GenBank.Scanner.InsdcScanner method) parse_children() (Bio.Phylo.CDAOIO.Parser method) parse_cigar() (Bio.Align.tabular.AlignmentIterator 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.SimpleLocation property) partsize (Bio.Align.Applications.MafftCommandline property) parttree (Bio.Align.Applications.MafftCommandline property) path (Bio.Align.Alignment 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_date() (in module Bio.PDB.PICIO)

PDB_REF (Bio.PDB.PDBList.PDBList attribute) pdb_residue_string() (Bio.PDB.internal_coords.IC_Residue method) PdbAtomIterator() (in module Bio.SeqIO.PdbIO) PDBConstructionException PDBConstructionWarning PDBException PDBIO (class in Bio.PDB.PDBIO) PDBIOException 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) pic_accuracy (Bio.PDB.internal_coords.IC_Residue attribute) pic_flags (Bio.PDB.internal_coords.IC_Residue attribute) picFlagsDefault (Bio.PDB.internal_coords.IC_Residue attribute) picFlagsDict (Bio.PDB.internal_coords.IC_Residue attribute) 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) pos_specific_score_matrix() (Bio.Align.AlignInfo.SummaryInfo method) position (Bio.SeqFeature.BetweenPosition property) (Bio.SeqFeature.OneOfPosition property) (Bio.SeqFeature.Position property) (Bio.SeqFeature.UnknownPosition property) (Bio.SeqFeature.WithinPosition property) Position (class in Bio.SeqFeature) 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_index() (Bio.SeqUtils.CodonUsage.CodonAdaptationIndex method) print_info_content() (in module Bio.Align.AlignInfo) 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) propagate_changes() (Bio.PDB.internal_coords.IC_Chain method) 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 (Bio.motifs.Motif property) PSSM (class in Bio.Align.AlignInfo) 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) qcp() (in module Bio.PDB.qcprot) QCPSuperimposer (class in Bio.PDB.qcprot) (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.Align.Alignment 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) query_coverage() (Bio.Compass.Record method) QUERY_GAP (Bio.Align.tabular.State attribute) 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) range() (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 (Bio.KEGG.KGML.KGML_pathway.Entry property) Reaction (class in Bio.KEGG.KGML.KGML_pathway) (class in Bio.Pathway) reaction_entries (Bio.KEGG.KGML.KGML_pathway.Pathway property) reactions (Bio.KEGG.KGML.KGML_pathway.Pathway property) reactions() (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) (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_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_next() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) read_PIC() (in module Bio.PDB.PICIO) read_PIC_seq() (in module Bio.PDB.PICIO) 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 (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 (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) 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) 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.Seq.MutableSeq method) (BioSQL.Loader.DatabaseRemover method) remove_component() (Bio.KEGG.KGML.KGML_pathway.Entry 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() (Bio.Seq.SequenceDataAbstractBaseClass method) 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) 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) rest() (Bio.Nexus.Nexus.CharBuffer method) retree (Bio.Align.Applications.MafftCommandline property) retrieve_assembly_file() (Bio.PDB.PDBList.PDBList method) retrieve_pdb_file() (Bio.PDB.PDBList.PDBList method) reverse (Bio.Emboss.Applications.Est2GenomeCommandline property) reverse() (Bio.Pathway.Reaction method) (Bio.Seq.MutableSeq method) reverse_complement() (Bio.motifs.Instances method) (Bio.motifs.matrix.GenericPositionMatrix method) (Bio.motifs.Motif method) (Bio.SeqRecord.SeqRecord method) (in module Bio.Seq) reverse_complement_rna() (in module Bio.Seq) reverseinput (Bio.Emboss.Applications.Primer3Commandline property) reward (Bio.Blast.Applications.NcbiblastnCommandline property) rewriteformat (Bio.Emboss.Applications.FSeqBootCommandline property) rfind() (Bio.Seq.SequenceDataAbstractBaseClass 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.SequenceDataAbstractBaseClass 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.SequenceDataAbstractBaseClass method) rstrip() (Bio.Seq.SequenceDataAbstractBaseClass method) rt (class in Bio.Sequencing.Ace) run() (Bio.PDB.qcprot.QCPSuperimposer method) (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.pairwise2.Alignment attribute) score() (Bio.Align.PairwiseAligner method) ScoreDistribution (class in Bio.motifs.thresholds) scorefile (Bio.Align.Applications.MuscleCommandline property) Scorer (class in Bio.Phylo.TreeConstruction) search (Bio.Phylo.Applications.PhymlCommandline property) search() (Bio.Align.bigbed.AlignmentIterator method) (Bio.AlignIO.MafIO.MafIndex method) (Bio.motifs.Instances method) (Bio.motifs.matrix.PositionSpecificScoringMatrix method) (Bio.PDB.NeighborSearch.NeighborSearch method) (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 (Bio.SeqRecord.SeqRecord property) (BioSQL.BioSeq.DBSeqRecord property) Seq (class in Bio.Seq) seq1() (in module Bio.SeqUtils) seq3() (in module Bio.SeqUtils) SEQ_TYPES (Bio.Align.Applications.TCoffeeCommandline attribute) seqA (Bio.pairwise2.Alignment attribute) seqall (Bio.Emboss.Applications.PrimerSearchCommandline property) seqB (Bio.pairwise2.Alignment attribute) 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) 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 (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) Sequence (class in Bio.Phylo.PhyloXML) sequence() (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) SequenceDataAbstractBaseClass (class in Bio.Seq) 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) SeqXmlIterator (class in Bio.SeqIO.SeqXmlIO) SeqXmlWriter (class in Bio.SeqIO.SeqXmlIO) set() (Bio.Nexus.Nexus.StepMatrix method) (Bio.PDB.qcprot.QCPSuperimposer 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.qcprot.QCPSuperimposer method) (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_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_reference() (Bio.PDB.cealign.CEAligner 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) SffIterator (class in Bio.SeqIO.SffIO) SffWriter (class in Bio.SeqIO.SffIO) sformat (Bio.Emboss.Applications.SeqretCommandline property) shape (Bio.Align.Alignment 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) ShrakeRupley (class in Bio.PDB.SASA) 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) SimpleLocation (class in Bio.SeqFeature) 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.Alignment method) (Bio.Align.MultipleSeqAlignment method) (Bio.Cluster.Tree method) (Bio.PDB.Residue.DisorderedResidue 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.SequenceDataAbstractBaseClass method) split_akl() (Bio.PDB.internal_coords.IC_Residue 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) 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.pairwise2.Alignment attribute) (Bio.SeqFeature.CompoundLocation property) (Bio.SeqFeature.SimpleLocation property) 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.SequenceDataAbstractBaseClass method) State (class in Bio.Align.tabular) Statistics (class in Bio.Wise.dnal) stats (Bio.Align.Applications.ClustalwCommandline property) status_characters (Bio.Align.maf.AlignmentIterator attribute) 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) (Bio.Entrez.Parser.OrderedListElement 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.SeqFeature property) (Bio.SeqFeature.SimpleLocation 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.SequenceDataAbstractBaseClass 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) substitutions (Bio.Align.Alignment property) (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) 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.Align.Alignment property) (Bio.Emboss.Applications.Primer3Commandline property) TARGET_GAP (Bio.Align.tabular.State attribute) 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 (Bio.Phylo.PhyloXML.Clade property) Taxonomy (class in Bio.Phylo.PhyloXML) taxonomy() (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_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) top (Bio.Phylo.Applications.FastTreeCommandline property) topdiags (Bio.Align.Applications.ClustalwCommandline property) topm (Bio.Phylo.Applications.FastTreeCommandline property) toSeq() (Bio.codonalign.codonseq.CodonSeq method) tossgaps (Bio.Align.Applications.ClustalwCommandline property) 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) train() (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() (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) translate() (Bio.codonalign.codonseq.CodonSeq method) (Bio.Graphics.GenomeDiagram.ColorTranslator method) (Bio.Seq.SequenceDataAbstractBaseClass 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 (Bio.Align.Applications.ClustalwCommandline property) (Bio.Align.Applications.PrankCommandline 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) 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) twice (Bio.Align.Applications.PrankCommandline property) TwoBitIterator (class in Bio.SeqIO.TwoBitIO) type (Bio.Align.Applications.ClustalwCommandline property) (Bio.Align.Applications.TCoffeeCommandline property) (Bio.Align.bigbed.Field attribute) type() (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) UndefinedSequenceError unfold_entities() (in module Bio.PDB.Selection) ungap() (Bio.codonalign.codonseq.CodonSeq method) (Bio.Seq.Seq 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) unlink() (Bio.Nexus.Nodes.Chain method) unroot() (Bio.Nexus.Trees.Tree method) update() (Bio.Align.substitution_matrices.Array method)

update_dCoordSpace() (Bio.PDB.internal_coords.IC_Chain 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.SequenceDataAbstractBaseClass 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) ValidationError value (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Phylo.PhyloXML.Confidence property) value() (Bio.Phylo.PhyloXMLIO.Writer method) values() (Bio.Align.substitution_matrices.Array 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) version() (in module Bio.PDB.DSSP) viterbi (Bio.Align.Applications.ProbconsCommandline property) viterbi() (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) width() (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) 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.Align) (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.Align.nexus.AlignmentWriter method) (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_alignments() (Bio.Align.a2m.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.nexus.AlignmentWriter 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.Align.interfaces.AlignmentWriter method) (Bio.Align.mauve.AlignmentWriter method) (Bio.Align.nexus.AlignmentWriter method) (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.NibIO.NibWriter method) (Bio.SeqIO.SffIO.SffWriter method) (Bio.SeqIO.XdnaIO.XdnaWriter method) write_footer() (Bio.Align.exonerate.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method) (Bio.SeqIO.Interfaces.SequenceWriter method) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter method) write_header() (Bio.Align.clustal.AlignmentWriter method) (Bio.Align.exonerate.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.maf.AlignmentWriter method) (Bio.Align.mauve.AlignmentWriter method) (Bio.Align.psl.AlignmentWriter method) (Bio.Align.sam.AlignmentWriter method) (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method) (Bio.AlignIO.MafIO.MafWriter method) (Bio.NMR.xpktools.Peaklist method) (Bio.SeqIO.Interfaces.SequenceWriter 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_multiple_alignments() (Bio.Align.interfaces.AlignmentWriter 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() (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.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) write_SCAD() (in module Bio.PDB.SCADIO) write_single_alignment() (Bio.Align.interfaces.AlignmentWriter method) 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)