Table of contents
Biopython Tutorial & Cookbook
API documentation
Biopython
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
_
__abstractmethods__ (Bio.Align.a2m.AlignmentIterator attribute)
(Bio.Align.a2m.AlignmentWriter attribute)
(Bio.Align.Alignments attribute)
(Bio.Align.AlignmentsAbstractBaseClass attribute)
(Bio.Align.bed.AlignmentIterator attribute)
(Bio.Align.bed.AlignmentWriter attribute)
(Bio.Align.bigbed.AlignmentIterator attribute)
(Bio.Align.bigbed.AlignmentWriter attribute)
(Bio.Align.bigmaf.AlignmentIterator attribute)
(Bio.Align.bigmaf.AlignmentWriter attribute)
(Bio.Align.bigpsl.AlignmentIterator attribute)
(Bio.Align.bigpsl.AlignmentWriter attribute)
(Bio.Align.chain.AlignmentIterator attribute)
(Bio.Align.chain.AlignmentWriter 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.PairwiseAlignments 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.Blast.Hit attribute)
(Bio.Blast.Records 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.AceIO.AceIterator attribute)
(Bio.SeqIO.AlignmentSequenceIterator attribute)
(Bio.SeqIO.AlignmentSequenceWriter attribute)
(Bio.SeqIO.FastaIO.FastaBlastIterator attribute)
(Bio.SeqIO.FastaIO.FastaIterator attribute)
(Bio.SeqIO.FastaIO.FastaPearsonIterator attribute)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute)
(Bio.SeqIO.FastaIO.FastaTwoLineWriter attribute)
(Bio.SeqIO.FastaIO.FastaWriter attribute)
(Bio.SeqIO.GckIO.GckIterator attribute)
(Bio.SeqIO.GfaIO.Gfa1Iterator attribute)
(Bio.SeqIO.GfaIO.Gfa2Iterator attribute)
(Bio.SeqIO.IgIO.IgIterator attribute)
(Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator attribute)
(Bio.SeqIO.InsdcIO.EmblIterator attribute)
(Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator attribute)
(Bio.SeqIO.InsdcIO.GenBankIterator attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
(Bio.SeqIO.InsdcIO.ImgtIterator attribute)
(Bio.SeqIO.InsdcIO.ImgtWriter attribute)
(Bio.SeqIO.Interfaces.SequenceIterator attribute)
(Bio.SeqIO.Interfaces.SequenceWriter attribute)
(Bio.SeqIO.NibIO.NibIterator attribute)
(Bio.SeqIO.NibIO.NibWriter attribute)
(Bio.SeqIO.PdbIO.CifAtomIterator attribute)
(Bio.SeqIO.PdbIO.CifSeqresIterator attribute)
(Bio.SeqIO.PdbIO.PdbAtomIterator attribute)
(Bio.SeqIO.PdbIO.PdbSeqresIterator attribute)
(Bio.SeqIO.PhdIO.PhdIterator attribute)
(Bio.SeqIO.PhdIO.PhdWriter attribute)
(Bio.SeqIO.PirIO.PirIterator attribute)
(Bio.SeqIO.PirIO.PirWriter attribute)
(Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute)
(Bio.SeqIO.QualityIO.FastqIlluminaWriter attribute)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute)
(Bio.SeqIO.QualityIO.FastqPhredIterator attribute)
(Bio.SeqIO.QualityIO.FastqPhredWriter attribute)
(Bio.SeqIO.QualityIO.FastqSolexaIterator attribute)
(Bio.SeqIO.QualityIO.FastqSolexaWriter attribute)
(Bio.SeqIO.QualityIO.QualPhredIterator attribute)
(Bio.SeqIO.QualityIO.QualPhredWriter attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter attribute)
(Bio.SeqIO.SffIO.SffIterator attribute)
(Bio.SeqIO.SffIO.SffWriter attribute)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute)
(Bio.SeqIO.SwissIO.SwissIterator attribute)
(Bio.SeqIO.TabIO.TabIterator attribute)
(Bio.SeqIO.TabIO.TabWriter attribute)
(Bio.SeqIO.TwoBitIO.TwoBitIterator attribute)
(Bio.SeqIO.UniprotIO.UniprotIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaWriter attribute)
__add__() (Bio.Align.Alignment method)
(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.Align.a2m.AlignmentIterator attribute)
(Bio.Align.a2m.AlignmentWriter attribute)
(Bio.Align.Alignments attribute)
(Bio.Align.bed.AlignmentIterator attribute)
(Bio.Align.bed.AlignmentWriter attribute)
(Bio.Align.bigbed.AlignmentIterator attribute)
(Bio.Align.bigbed.AlignmentWriter attribute)
(Bio.Align.bigbed.AutoSQLTable attribute)
(Bio.Align.bigmaf.AlignmentIterator attribute)
(Bio.Align.bigmaf.AlignmentWriter attribute)
(Bio.Align.bigpsl.AlignmentIterator attribute)
(Bio.Align.bigpsl.AlignmentWriter attribute)
(Bio.Align.chain.AlignmentIterator attribute)
(Bio.Align.chain.AlignmentWriter 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.PairwiseAlignments 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.AlignIO.EmbossIO.EmbossIterator attribute)
(Bio.AlignIO.Interfaces.AlignmentIterator attribute)
(Bio.AlignIO.Interfaces.AlignmentWriter attribute)
(Bio.AlignIO.Interfaces.SequentialAlignmentWriter attribute)
(Bio.AlignIO.MafIO.MafWriter attribute)
(Bio.AlignIO.MauveIO.MauveIterator attribute)
(Bio.AlignIO.MauveIO.MauveWriter attribute)
(Bio.AlignIO.MsfIO.MsfIterator attribute)
(Bio.AlignIO.NexusIO.NexusWriter attribute)
(Bio.AlignIO.PhylipIO.PhylipIterator attribute)
(Bio.AlignIO.PhylipIO.PhylipWriter attribute)
(Bio.AlignIO.PhylipIO.RelaxedPhylipIterator attribute)
(Bio.AlignIO.PhylipIO.RelaxedPhylipWriter attribute)
(Bio.AlignIO.PhylipIO.SequentialPhylipIterator attribute)
(Bio.AlignIO.PhylipIO.SequentialPhylipWriter attribute)
(Bio.AlignIO.StockholmIO.StockholmIterator attribute)
(Bio.AlignIO.StockholmIO.StockholmWriter attribute)
(Bio.BiopythonDeprecationWarning attribute)
(Bio.BiopythonExperimentalWarning attribute)
(Bio.BiopythonParserWarning attribute)
(Bio.Blast.Hit attribute)
(Bio.Blast.HSP attribute)
(Bio.Blast.NCBIXML.Blast attribute)
(Bio.Blast.NCBIXML.DescriptionExt attribute)
(Bio.Blast.NCBIXML.PSIBlast attribute)
(Bio.codonalign.codonalignment.CodonAlignment attribute)
(Bio.codonalign.codonseq.CodonSeq attribute)
(Bio.Data.CodonTable.AmbiguousCodonTable attribute)
(Bio.Data.CodonTable.CodonTable attribute)
(Bio.Data.CodonTable.NCBICodonTable attribute)
(Bio.Data.CodonTable.NCBICodonTableDNA attribute)
(Bio.Data.CodonTable.NCBICodonTableRNA attribute)
(Bio.Entrez.Parser.DataHandlerMeta attribute)
(Bio.ExPASy.ScanProsite.ContentHandler attribute)
(Bio.GenBank.Scanner.EmblScanner attribute)
(Bio.GenBank.Scanner.GenBankScanner attribute)
(Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment attribute)
(Bio.Graphics.BasicChromosome.Chromosome attribute)
(Bio.Graphics.BasicChromosome.ChromosomeSegment attribute)
(Bio.Graphics.BasicChromosome.SpacerSegment attribute)
(Bio.Graphics.BasicChromosome.TelomereSegment attribute)
(Bio.HMM.DynamicProgramming.LogDPAlgorithms attribute)
(Bio.HMM.DynamicProgramming.ScaledDPAlgorithms attribute)
(Bio.HMM.Trainer.BaumWelchTrainer attribute)
(Bio.HMM.Trainer.KnownStateTrainer attribute)
(Bio.MissingPythonDependencyError attribute)
(Bio.motifs.jaspar.Motif attribute)
(Bio.motifs.matrix.FrequencyPositionMatrix attribute)
(Bio.motifs.matrix.PositionSpecificScoringMatrix attribute)
(Bio.motifs.matrix.PositionWeightMatrix attribute)
(Bio.motifs.meme.Instance attribute)
(Bio.motifs.meme.Motif attribute)
(Bio.motifs.transfac.Motif attribute)
(Bio.Nexus.Trees.Tree attribute)
(Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap attribute)
(Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap attribute)
(Bio.PDB.Chain.Chain attribute)
(Bio.PDB.DSSP.DSSP attribute)
(Bio.PDB.Entity.DisorderedEntityWrapper attribute)
(Bio.PDB.Entity.Entity attribute)
(Bio.PDB.HSExposure.ExposureCN attribute)
(Bio.PDB.HSExposure.HSExposureCA attribute)
(Bio.PDB.HSExposure.HSExposureCB attribute)
(Bio.PDB.internal_coords.Dihedron attribute)
(Bio.PDB.internal_coords.Hedron attribute)
(Bio.PDB.internal_coords.IC_Chain attribute)
(Bio.PDB.internal_coords.IC_Residue attribute)
(Bio.PDB.mmcifio.MMCIFIO attribute)
(Bio.PDB.mmtf.mmtfio.MMTFIO attribute)
(Bio.PDB.Model.Model attribute)
(Bio.PDB.NACCESS.NACCESS attribute)
(Bio.PDB.NACCESS.NACCESS_atomic attribute)
(Bio.PDB.PDBExceptions.PDBConstructionWarning attribute)
(Bio.PDB.PDBIO.PDBIO attribute)
(Bio.PDB.Polypeptide.PPBuilder attribute)
(Bio.PDB.Residue.DisorderedResidue attribute)
(Bio.PDB.Residue.Residue attribute)
(Bio.PDB.ResidueDepth.ResidueDepth attribute)
(Bio.PDB.Structure.Structure attribute)
(Bio.Phylo.BaseTree.Clade attribute)
(Bio.Phylo.BaseTree.Tree attribute)
(Bio.Phylo.CDAO.Clade attribute)
(Bio.Phylo.CDAO.Tree attribute)
(Bio.Phylo.Newick.Clade attribute)
(Bio.Phylo.Newick.Tree attribute)
(Bio.Phylo.NeXML.Clade attribute)
(Bio.Phylo.NeXML.Tree attribute)
(Bio.Phylo.PAML.codeml.Codeml attribute)
(Bio.Phylo.PAML.yn00.Yn00 attribute)
(Bio.Phylo.PhyloXML.Accession attribute)
(Bio.Phylo.PhyloXML.Annotation attribute)
(Bio.Phylo.PhyloXML.BinaryCharacters attribute)
(Bio.Phylo.PhyloXML.BranchColor attribute)
(Bio.Phylo.PhyloXML.Clade attribute)
(Bio.Phylo.PhyloXML.CladeRelation attribute)
(Bio.Phylo.PhyloXML.Confidence attribute)
(Bio.Phylo.PhyloXML.Date attribute)
(Bio.Phylo.PhyloXML.Distribution attribute)
(Bio.Phylo.PhyloXML.DomainArchitecture attribute)
(Bio.Phylo.PhyloXML.Events attribute)
(Bio.Phylo.PhyloXML.Id attribute)
(Bio.Phylo.PhyloXML.MolSeq attribute)
(Bio.Phylo.PhyloXML.Other attribute)
(Bio.Phylo.PhyloXML.PhyloElement attribute)
(Bio.Phylo.PhyloXML.Phylogeny attribute)
(Bio.Phylo.PhyloXML.Phyloxml attribute)
(Bio.Phylo.PhyloXML.PhyloXMLWarning attribute)
(Bio.Phylo.PhyloXML.Point attribute)
(Bio.Phylo.PhyloXML.Polygon attribute)
(Bio.Phylo.PhyloXML.Property attribute)
(Bio.Phylo.PhyloXML.ProteinDomain attribute)
(Bio.Phylo.PhyloXML.Reference attribute)
(Bio.Phylo.PhyloXML.Sequence attribute)
(Bio.Phylo.PhyloXML.SequenceRelation attribute)
(Bio.Phylo.PhyloXML.Taxonomy attribute)
(Bio.Phylo.PhyloXML.Uri attribute)
(Bio.Phylo.TreeConstruction.DistanceTreeConstructor attribute)
(Bio.Phylo.TreeConstruction.NNITreeSearcher attribute)
(Bio.Phylo.TreeConstruction.ParsimonyScorer attribute)
(Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor attribute)
(Bio.SCOP.Domain 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_domtab.Hmmer3DomtabHmmqueryParser attribute)
(Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter attribute)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer attribute)
(Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser 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.AceIO.AceIterator attribute)
(Bio.SeqIO.AlignmentSequenceIterator attribute)
(Bio.SeqIO.AlignmentSequenceWriter attribute)
(Bio.SeqIO.FastaIO.FastaBlastIterator attribute)
(Bio.SeqIO.FastaIO.FastaIterator attribute)
(Bio.SeqIO.FastaIO.FastaPearsonIterator attribute)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute)
(Bio.SeqIO.FastaIO.FastaTwoLineWriter attribute)
(Bio.SeqIO.FastaIO.FastaWriter attribute)
(Bio.SeqIO.GckIO.GckIterator attribute)
(Bio.SeqIO.GfaIO.Gfa1Iterator attribute)
(Bio.SeqIO.GfaIO.Gfa2Iterator attribute)
(Bio.SeqIO.IgIO.IgIterator attribute)
(Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator attribute)
(Bio.SeqIO.InsdcIO.EmblIterator attribute)
(Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator attribute)
(Bio.SeqIO.InsdcIO.GenBankIterator attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
(Bio.SeqIO.InsdcIO.ImgtIterator attribute)
(Bio.SeqIO.InsdcIO.ImgtWriter attribute)
(Bio.SeqIO.Interfaces.SequenceIterator attribute)
(Bio.SeqIO.Interfaces.SequenceWriter attribute)
(Bio.SeqIO.NibIO.NibIterator attribute)
(Bio.SeqIO.NibIO.NibWriter attribute)
(Bio.SeqIO.PdbIO.CifAtomIterator attribute)
(Bio.SeqIO.PdbIO.CifSeqresIterator attribute)
(Bio.SeqIO.PdbIO.PdbAtomIterator attribute)
(Bio.SeqIO.PdbIO.PdbSeqresIterator attribute)
(Bio.SeqIO.PhdIO.PhdIterator attribute)
(Bio.SeqIO.PhdIO.PhdWriter attribute)
(Bio.SeqIO.PirIO.PirIterator attribute)
(Bio.SeqIO.PirIO.PirWriter attribute)
(Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute)
(Bio.SeqIO.QualityIO.FastqIlluminaWriter attribute)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute)
(Bio.SeqIO.QualityIO.FastqPhredIterator attribute)
(Bio.SeqIO.QualityIO.FastqPhredWriter attribute)
(Bio.SeqIO.QualityIO.FastqSolexaIterator attribute)
(Bio.SeqIO.QualityIO.FastqSolexaWriter attribute)
(Bio.SeqIO.QualityIO.InvalidCharError attribute)
(Bio.SeqIO.QualityIO.QualPhredIterator attribute)
(Bio.SeqIO.QualityIO.QualPhredWriter attribute)
(Bio.SeqIO.SeqXmlIO.ContentHandler attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter attribute)
(Bio.SeqIO.SffIO.SffIterator attribute)
(Bio.SeqIO.SffIO.SffWriter attribute)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute)
(Bio.SeqIO.SwissIO.SwissIterator attribute)
(Bio.SeqIO.TabIO.TabIterator attribute)
(Bio.SeqIO.TabIO.TabWriter attribute)
(Bio.SeqIO.TwoBitIO.TwoBitIterator attribute)
(Bio.SeqIO.UniprotIO.UniprotIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaWriter attribute)
(Bio.SeqRecord.SeqRecord attribute)
(Bio.SwissProt.FeatureTable attribute)
(BioSQL.BioSeq.DBSeqRecord attribute)
(BioSQL.BioSeqDatabase.MysqlConnectorAdaptor attribute)
(BioSQL.DBUtils.Mysql_dbutils attribute)
(BioSQL.DBUtils.Pgdb_dbutils attribute)
(BioSQL.DBUtils.Psycopg2_dbutils attribute)
(BioSQL.DBUtils.Sqlite_dbutils 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.Align.bigbed.AutoSQLTable method)
(Bio.Seq.SequenceDataAbstractBaseClass method)
(Bio.SeqRecord.SeqRecord method)
__call__() (Bio.pairwise2.affine_penalty method)
(Bio.pairwise2.dictionary_match method)
(Bio.pairwise2.identity_match method)
__contains__() (Bio.Align.substitution_matrices.Array method)
(Bio.Blast.Record 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)
__dataclass_fields__ (Bio.SeqIO.QualityIO.InvalidCharError attribute)
__dataclass_params__ (Bio.SeqIO.QualityIO.InvalidCharError attribute)
__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.Align.MultipleSeqAlignment method)
(Bio.PDB.Chain.Chain method)
(Bio.PDB.Entity.Entity method)
(Bio.phenotype.phen_micro.PlateRecord method)
(Bio.Phylo.PhyloXML.Events method)
(Bio.Seq.MutableSeq method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
__enter__() (Bio.Align.interfaces.AlignmentIterator method)
(Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
(Bio.Blast.Records method)
(Bio.SeqIO.Interfaces.SequenceIterator 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.SeqIO.QualityIO.InvalidCharError method)
(Bio.SeqRecord.SeqRecord method)
__exit__() (Bio.Align.interfaces.AlignmentIterator method)
(Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
(Bio.Blast.Records method)
(Bio.SeqIO.Interfaces.SequenceIterator 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.Alignment method)
(Bio.Align.bigbed.AutoSQLTable method)
(Bio.Align.interfaces.AlignmentIterator method)
(Bio.Align.MultipleSeqAlignment method)
(Bio.Align.PairwiseAlignments method)
(Bio.Align.substitution_matrices.Array method)
(Bio.Blast.Hit method)
(Bio.Blast.Record method)
(Bio.Blast.Records 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.motifs.Motif method)
(Bio.motifs.transfac.Motif 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.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.SeqIO.QualityIO.InvalidCharError 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.SummaryInfo method)
(Bio.Align.Alignment method)
(Bio.Align.AlignmentCounts method)
(Bio.Align.Alignments method)
(Bio.Align.bed.AlignmentWriter method)
(Bio.Align.bigbed.AlignmentWriter method)
(Bio.Align.bigbed.AutoSQLTable method)
(Bio.Align.bigmaf.AlignmentIterator method)
(Bio.Align.bigmaf.AlignmentWriter method)
(Bio.Align.bigpsl.AlignmentWriter method)
(Bio.Align.CodonAligner 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.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.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
(Bio.Blast.CorruptedXMLError method)
(Bio.Blast.NCBIXML.Alignment method)
(Bio.Blast.NCBIXML.Blast method)
(Bio.Blast.NCBIXML.BlastParser method)
(Bio.Blast.NCBIXML.DatabaseReport method)
(Bio.Blast.NCBIXML.Description method)
(Bio.Blast.NCBIXML.DescriptionExt method)
(Bio.Blast.NCBIXML.DescriptionExtItem method)
(Bio.Blast.NCBIXML.Header method)
(Bio.Blast.NCBIXML.HSP method)
(Bio.Blast.NCBIXML.MultipleAlignment method)
(Bio.Blast.NCBIXML.Parameters method)
(Bio.Blast.NCBIXML.PSIBlast method)
(Bio.Blast.NCBIXML.Round method)
(Bio.Blast.NotXMLError method)
(Bio.Blast.Record method)
(Bio.Blast.Records 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.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.motifs.alignace.Record 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.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.binary_cif.BinaryCIFParser 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.PDBMLParser.PDBMLParser 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.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.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.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_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.Reference method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqFeature.SimpleLocation method)
(Bio.SeqIO.AbiIO.AbiIterator method)
(Bio.SeqIO.AceIO.AceIterator method)
(Bio.SeqIO.AlignmentSequenceIterator method)
(Bio.SeqIO.FastaIO.FastaBlastIterator method)
(Bio.SeqIO.FastaIO.FastaIterator method)
(Bio.SeqIO.FastaIO.FastaPearsonIterator method)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)
(Bio.SeqIO.FastaIO.FastaTwoLineWriter method)
(Bio.SeqIO.FastaIO.FastaWriter method)
(Bio.SeqIO.GckIO.GckIterator method)
(Bio.SeqIO.GfaIO.Gfa1Iterator method)
(Bio.SeqIO.GfaIO.Gfa2Iterator 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.PdbIO.CifAtomIterator method)
(Bio.SeqIO.PdbIO.CifSeqresIterator method)
(Bio.SeqIO.PdbIO.PdbAtomIterator method)
(Bio.SeqIO.PdbIO.PdbSeqresIterator method)
(Bio.SeqIO.PhdIO.PhdIterator method)
(Bio.SeqIO.PirIO.PirIterator method)
(Bio.SeqIO.PirIO.PirWriter method)
(Bio.SeqIO.QualityIO.FastqIlluminaIterator method)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass method)
(Bio.SeqIO.QualityIO.FastqPhredIterator method)
(Bio.SeqIO.QualityIO.FastqSolexaIterator method)
(Bio.SeqIO.QualityIO.InvalidCharError 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.SwissIO.SwissIterator method)
(Bio.SeqIO.TabIO.TabIterator method)
(Bio.SeqIO.TwoBitIO.TwoBitIterator method)
(Bio.SeqIO.UniprotIO.UniprotIterator method)
(Bio.SeqIO.XdnaIO.XdnaIterator 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.Phd.Record method)
(Bio.SeqUtils.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)
(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.AlignmentsAbstractBaseClass method)
(Bio.Align.MultipleSeqAlignment method)
(Bio.AlignIO.Interfaces.AlignmentIterator method)
(Bio.bgzf.BgzfReader method)
(Bio.Blast.Records 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_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.Alignments method)
(Bio.Align.AlignmentsAbstractBaseClass method)
(Bio.Align.bigbed.AlignmentIterator method)
(Bio.Align.hhr.AlignmentIterator method)
(Bio.Align.interfaces.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)
__match_args__ (Bio.Align.bigbed.Field attribute)
(Bio.pairwise2.Alignment attribute)
(Bio.SeqIO.QualityIO.InvalidCharError attribute)
__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.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.Alignments method)
(Bio.Align.AlignmentsAbstractBaseClass method)
(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.Records method)
(Bio.GenBank.Iterator method)
(Bio.Nexus.Nexus.CharBuffer method)
(Bio.Nexus.StandardData.StandardData method)
(Bio.SeqIO.AbiIO.AbiIterator method)
(Bio.SeqIO.AceIO.AceIterator method)
(Bio.SeqIO.AlignmentSequenceIterator method)
(Bio.SeqIO.FastaIO.FastaBlastIterator method)
(Bio.SeqIO.FastaIO.FastaIterator method)
(Bio.SeqIO.FastaIO.FastaPearsonIterator method)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator method)
(Bio.SeqIO.GckIO.GckIterator method)
(Bio.SeqIO.GfaIO.Gfa1Iterator method)
(Bio.SeqIO.GfaIO.Gfa2Iterator 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.CifAtomIterator method)
(Bio.SeqIO.PdbIO.CifSeqresIterator method)
(Bio.SeqIO.PdbIO.PdbAtomIterator method)
(Bio.SeqIO.PdbIO.PdbSeqresIterator method)
(Bio.SeqIO.PhdIO.PhdIterator method)
(Bio.SeqIO.PirIO.PirIterator method)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass method)
(Bio.SeqIO.QualityIO.QualPhredIterator method)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator method)
(Bio.SeqIO.SffIO.SffIterator method)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator method)
(Bio.SeqIO.SwissIO.SwissIterator method)
(Bio.SeqIO.TabIO.TabIterator method)
(Bio.SeqIO.TwoBitIO.TwoBitIterator method)
(Bio.SeqIO.UniprotIO.UniprotIterator method)
(Bio.SeqIO.XdnaIO.XdnaIterator method)
__nonzero__() (Bio.SeqFeature.CompoundLocation method)
(Bio.SeqFeature.SimpleLocation method)
__orig_bases__ (Bio.PDB.Chain.Chain attribute)
(Bio.PDB.Entity.Entity attribute)
(Bio.PDB.Model.Model attribute)
(Bio.PDB.Residue.Residue attribute)
(Bio.PDB.Structure.Structure attribute)
(Bio.SeqIO.Interfaces.SequenceIterator attribute)
(Bio.SeqIO.Interfaces.SequenceWriter attribute)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute)
__parameters__ (Bio.PDB.Chain.Chain attribute)
(Bio.PDB.Entity.Entity attribute)
(Bio.PDB.Model.Model attribute)
(Bio.PDB.Residue.Residue attribute)
(Bio.PDB.Structure.Structure attribute)
(Bio.SeqIO.AbiIO.AbiIterator attribute)
(Bio.SeqIO.AceIO.AceIterator attribute)
(Bio.SeqIO.AlignmentSequenceIterator attribute)
(Bio.SeqIO.AlignmentSequenceWriter attribute)
(Bio.SeqIO.FastaIO.FastaBlastIterator attribute)
(Bio.SeqIO.FastaIO.FastaIterator attribute)
(Bio.SeqIO.FastaIO.FastaPearsonIterator attribute)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute)
(Bio.SeqIO.FastaIO.FastaTwoLineWriter attribute)
(Bio.SeqIO.FastaIO.FastaWriter attribute)
(Bio.SeqIO.GckIO.GckIterator attribute)
(Bio.SeqIO.GfaIO.Gfa1Iterator attribute)
(Bio.SeqIO.GfaIO.Gfa2Iterator attribute)
(Bio.SeqIO.IgIO.IgIterator attribute)
(Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator attribute)
(Bio.SeqIO.InsdcIO.EmblIterator attribute)
(Bio.SeqIO.InsdcIO.EmblWriter attribute)
(Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator attribute)
(Bio.SeqIO.InsdcIO.GenBankIterator attribute)
(Bio.SeqIO.InsdcIO.GenBankWriter attribute)
(Bio.SeqIO.InsdcIO.ImgtIterator attribute)
(Bio.SeqIO.InsdcIO.ImgtWriter attribute)
(Bio.SeqIO.Interfaces.SequenceIterator attribute)
(Bio.SeqIO.Interfaces.SequenceWriter attribute)
(Bio.SeqIO.NibIO.NibIterator attribute)
(Bio.SeqIO.NibIO.NibWriter attribute)
(Bio.SeqIO.PdbIO.CifAtomIterator attribute)
(Bio.SeqIO.PdbIO.CifSeqresIterator attribute)
(Bio.SeqIO.PdbIO.PdbAtomIterator attribute)
(Bio.SeqIO.PdbIO.PdbSeqresIterator attribute)
(Bio.SeqIO.PhdIO.PhdIterator attribute)
(Bio.SeqIO.PhdIO.PhdWriter attribute)
(Bio.SeqIO.PirIO.PirIterator attribute)
(Bio.SeqIO.PirIO.PirWriter attribute)
(Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute)
(Bio.SeqIO.QualityIO.FastqIlluminaWriter attribute)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute)
(Bio.SeqIO.QualityIO.FastqPhredIterator attribute)
(Bio.SeqIO.QualityIO.FastqPhredWriter attribute)
(Bio.SeqIO.QualityIO.FastqSolexaIterator attribute)
(Bio.SeqIO.QualityIO.FastqSolexaWriter attribute)
(Bio.SeqIO.QualityIO.QualPhredIterator attribute)
(Bio.SeqIO.QualityIO.QualPhredWriter attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter attribute)
(Bio.SeqIO.SffIO.SffIterator attribute)
(Bio.SeqIO.SffIO.SffWriter attribute)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute)
(Bio.SeqIO.SwissIO.SwissIterator attribute)
(Bio.SeqIO.TabIO.TabIterator attribute)
(Bio.SeqIO.TabIO.TabWriter attribute)
(Bio.SeqIO.TwoBitIO.TwoBitIterator attribute)
(Bio.SeqIO.UniprotIO.UniprotIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaWriter attribute)
__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.Blast.Hit method)
(Bio.Blast.HSP method)
(Bio.Blast.Record method)
(Bio.Blast.Records 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.Reference method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqFeature.SimpleLocation method)
(Bio.SeqFeature.UnknownPosition method)
(Bio.SeqFeature.WithinPosition method)
(Bio.SeqIO.QualityIO.InvalidCharError method)
(Bio.SeqRecord.SeqRecord method)
(Bio.UniGene.ProtsimLine method)
(Bio.UniGene.Record method)
(Bio.UniGene.SequenceLine method)
(Bio.UniGene.STSLine method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
__setattr__() (Bio.Align.PairwiseAligner 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.Alignment method)
(Bio.Align.bigbed.AutoSQLTable method)
(Bio.Align.MultipleSeqAlignment method)
(Bio.Align.substitution_matrices.Array method)
(Bio.Blast.CorruptedXMLError method)
(Bio.Blast.Hit method)
(Bio.Blast.HSP method)
(Bio.Blast.NCBIXML.Alignment method)
(Bio.Blast.NCBIXML.Description method)
(Bio.Blast.NCBIXML.DescriptionExtItem method)
(Bio.Blast.NCBIXML.HSP method)
(Bio.Blast.NotXMLError method)
(Bio.Blast.Record method)
(Bio.Blast.Records 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.motifs.clusterbuster.Record 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.Reference method)
(Bio.SeqFeature.SeqFeature method)
(Bio.SeqFeature.SimpleLocation method)
(Bio.SeqFeature.WithinPosition method)
(Bio.SeqIO.QualityIO.InvalidCharError method)
(Bio.SeqRecord.SeqRecord method)
(Bio.SeqUtils.CodonAdaptationIndex 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.Graphics.ColorSpiral.ColorSpiral property)
AAsiz (Bio.PDB.internal_coords.IC_Chain attribute)
AbiIterator (class in Bio.SeqIO.AbiIO)
AbstractAtomPropertyMap (class in Bio.PDB.AbstractPropertyMap)
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 (class in Bio.SeqIO.AceIO)
adam_consensus() (in module Bio.Phylo.Consensus)
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.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)
af (class in Bio.Sequencing.Ace)
affine_penalty (class in Bio.pairwise2)
AfterPosition (class in Bio.SeqFeature)
align() (Bio.Align.CodonAligner method)
(Bio.Align.PairwiseAligner method)
(Bio.PDB.cealign.CEAligner method)
aligned (Bio.Align.Alignment property)
(Bio.Align.AlignmentCounts property)
alignment (Bio.Align.MultipleSeqAlignment property)
(Bio.Phylo.PhyloXML.Phylogeny property)
Alignment (class in Bio.Align)
(class in Bio.Blast.NCBIXML)
(class in Bio.pairwise2)
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.chain)
(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)
Alignments (class in Bio.Align)
AlignmentsAbstractBaseClass (class in Bio.Align)
AlignmentSequenceIterator (class in Bio.SeqIO)
AlignmentSequenceWriter (class in Bio.SeqIO)
AlignmentWriter (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.chain)
(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)
allow_all_transitions() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
allow_transition() (Bio.HMM.MarkovModel.MarkovModelBuilder method)
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_acids_percent (Bio.SeqUtils.ProtParam.ProteinAnalysis property)
Amplifier (class in Bio.Emboss.PrimerSearch)
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)
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 (Bio.SeqRecord.SeqRecord attribute)
(BioSQL.BioSeq.DBSeqRecord property)
anticonsensus (Bio.motifs.matrix.GenericPositionMatrix property)
(Bio.motifs.Motif property)
append() (Bio.Align.MultipleSeqAlignment method)
(Bio.SCOP.Raf.SeqMap method)
(Bio.Seq.MutableSeq method)
append_item() (Bio.Blast.NCBIXML.DescriptionExt method)
append_sets() (Bio.Nexus.Nexus.Nexus method)
apply() (Bio.PDB.qcprot.QCPSuperimposer method)
(Bio.PDB.Superimposer.Superimposer method)
applyMtx() (Bio.PDB.internal_coords.IC_Residue method)
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)
as_type (Bio.Align.bigbed.Field attribute)
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)
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)
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)
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)
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)
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)
BinaryCharacters (class in Bio.Phylo.PhyloXML)
BinaryCIFParser (class in Bio.PDB.binary_cif)
Bio
module
Bio.Affy
module
Bio.Affy.CelFile
module
Bio.Align
module
Bio.Align.a2m
module
Bio.Align.AlignInfo
module
Bio.Align.analysis
module
Bio.Align.bed
module
Bio.Align.bigbed
module
Bio.Align.bigmaf
module
Bio.Align.bigpsl
module
Bio.Align.chain
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.bgzf
module
Bio.Blast
module
Bio.Blast.NCBIWWW
module
Bio.Blast.NCBIXML
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.Emboss
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.Medline
module
Bio.motifs
module
Bio.motifs.alignace
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.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.alphafold_db
module
Bio.PDB.Atom
module
Bio.PDB.binary_cif
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.PDBMLParser
module
Bio.PDB.PDBParser
module
Bio.PDB.PICIO
module
Bio.PDB.Polypeptide
module
Bio.PDB.PSEA
module
Bio.PDB.qcprot
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.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.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_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.GfaIO
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.Phd
module
Bio.SeqUtils
module
Bio.SeqUtils.CheckSum
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
BiopythonDeprecationWarning
BiopythonExperimentalWarning
BiopythonParserWarning
BiopythonWarning
BioSeqDatabase (class in BioSQL.BioSeqDatabase)
BioSQL
module
BioSQL.BioSeq
module
BioSQL.BioSeqDatabase
module
BioSQL.DBUtils
module
BioSQL.Loader
module
bits() (Bio.PDB.internal_coords.Dihedron method)
Blast (class in Bio.Blast.NCBIXML)
BlastParser (class in Bio.Blast.NCBIXML)
BlastTabIndexer (class in Bio.SearchIO.BlastIO.blast_tab)
BlastTabParser (class in Bio.SearchIO.BlastIO.blast_tab)
BlastTabWriter (class in Bio.SearchIO.BlastIO.blast_tab)
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)
blue() (Bio.Phylo.PhyloXMLIO.Writer method)
bond_rotate() (Bio.PDB.internal_coords.IC_Residue method)
bond_set() (Bio.PDB.internal_coords.IC_Residue method)
bootstrap() (Bio.Nexus.Nexus.Nexus method)
(in module Bio.Phylo.Consensus)
bootstrap_consensus() (in module Bio.Phylo.Consensus)
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)
branch_length() (Bio.Phylo.PhyloXMLIO.Writer method)
BranchColor (class in Bio.Phylo.BaseTree)
(class in Bio.Phylo.PhyloXML)
branchlength2support() (Bio.Nexus.Trees.Tree method)
bs (class in Bio.Sequencing.Ace)
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)
C
ca_depth() (in module Bio.PDB.ResidueDepth)
cal_dn_ds() (in module Bio.codonalign.codonseq)
calc_affine_penalty() (in module Bio.pairwise2)
calc_angle() (in module Bio.PDB.vectors)
calc_dihedral() (in module Bio.PDB.vectors)
calculate() (Bio.motifs.matrix.PositionSpecificScoringMatrix method)
(Bio.SeqUtils.CodonAdaptationIndex method)
calculate_consensus() (Bio.motifs.matrix.GenericPositionMatrix method)
calculate_dn_ds() (in module Bio.Align.analysis)
calculate_dn_ds_matrix() (in module Bio.Align.analysis)
calculate_pseudocounts() (in module Bio.motifs.jaspar)
CaPPBuilder (class in Bio.PDB.Polypeptide)
CAPSMap (class in Bio.CAPS)
cdao_to_obo() (in module Bio.Phylo.NeXMLIO)
cdf_chi2() (in module Bio.Phylo.PAML.chi2)
CEAligner (class in Bio.PDB.cealign)
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)
chem_correction() (in module Bio.SeqUtils.MeltingTemp)
child_dict (Bio.PDB.Entity.Entity attribute)
child_edges() (Bio.Pathway.Rep.Graph.Graph method)
(Bio.Pathway.Rep.MultiGraph.MultiGraph method)
child_list (Bio.PDB.Entity.Entity attribute)
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)
CifAtomIterator (class in Bio.SeqIO.PdbIO)
CifSeqresIterator (class in 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)
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.AlignIO.MafIO.MafIndex method)
(Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
(BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.DBServer method)
ClustalIterator (class in Bio.AlignIO.ClustalIO)
ClustalWriter (class in Bio.AlignIO.ClustalIO)
clustercentroids() (Bio.Cluster.Record method)
(in module Bio.Cluster)
clusterdistance() (Bio.Cluster.Record method)
(in module Bio.Cluster)
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
CodonAdaptationIndex (class in Bio.SeqUtils)
CodonAligner (class in Bio.Align)
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)
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)
ComparativeScatterPlot (class in Bio.Graphics.Comparative)
compare_residues() (in module Bio.PDB.ic_rebuild)
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)
ConsoleWidth (Bio.Restriction.PrintFormat.PrintFormat attribute)
constant() (Bio.Nexus.Nexus.Nexus method)
ContentHandler (class in Bio.ExPASy.ScanProsite)
(class in Bio.SeqIO.SeqXmlIO)
Contig (class in Bio.Sequencing.Ace)
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.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)
CorruptedXMLError
,
[1]
count() (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)
crop_matrix() (Bio.Nexus.Nexus.Nexus method)
CrossLink (class in Bio.Graphics.GenomeDiagram)
cstatus() (Bio.Nexus.Nexus.Nexus method)
CsvIterator() (in module Bio.phenotype.phen_micro)
ct (class in Bio.Sequencing.Ace)
cut() (Bio.Cluster.Tree method)
D
d2h (Bio.PDB.internal_coords.AtomKey attribute)
darken() (in module Bio.Graphics.KGML_vis)
data (Bio.Blast.Records property)
data_generator() (Bio.PopGen.GenePop.LargeFileParser.Record method)
data_quartiles() (Bio.Graphics.GenomeDiagram.GraphSet method)
data_table() (in module Bio.NMR.xpktools)
DatabaseLoader (class in BioSQL.Loader)
DatabaseRemover (class in BioSQL.Loader)
DatabaseReport (class in Bio.Blast.NCBIXML)
DataHandler (class in Bio.Entrez.Parser)
DataHandlerMeta (class in Bio.Entrez.Parser)
Date (class in Bio.Phylo.PhyloXML)
date() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
DBSeqRecord (class in BioSQL.BioSeq)
DBServer (class in BioSQL.BioSeqDatabase)
dbxrefs (Bio.SeqRecord.SeqRecord attribute)
(BioSQL.BioSeq.DBSeqRecord property)
dCoordSpace (Bio.PDB.internal_coords.IC_Chain attribute)
dcsValid (Bio.PDB.internal_coords.IC_Chain attribute)
decode() (Bio.Seq.SequenceDataAbstractBaseClass method)
default (Bio.Align.bigbed.AutoSQLTable attribute)
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)
deletions (Bio.Align.AlignmentCounts property)
depths() (Bio.Phylo.BaseTree.TreeMixin method)
desc() (Bio.Phylo.PhyloXMLIO.Writer method)
Description (class in Bio.Blast.NCBIXML)
description() (Bio.Phylo.PhyloXMLIO.Writer method)
DescriptionExt (class in Bio.Blast.NCBIXML)
DescriptionExtItem (class in Bio.Blast.NCBIXML)
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)
details (Bio.SeqIO.QualityIO.InvalidCharError attribute)
df_search() (in module Bio.Pathway.Rep.MultiGraph)
Diagram (class in Bio.Graphics.GenomeDiagram)
dictionary_match (class in Bio.pairwise2)
DictionaryElement (class in Bio.Entrez.Parser)
difference() (Bio.PDB.internal_coords.Dihedron method)
DifferentialCutsite (class in Bio.CAPS)
dihedral_signs() (Bio.PDB.internal_coords.IC_Chain method)
Dihedron (class in Bio.PDB.internal_coords)
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)
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)
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)
dna_models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute)
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)
DomainArchitecture (class in Bio.Phylo.PhyloXML)
domainsClusteredByEv() (Bio.SCOP.Astral method)
domainsClusteredById() (Bio.SCOP.Astral method)
download_all_assemblies() (Bio.PDB.PDBList.PDBList method)
download_cif_for() (in module Bio.PDB.alphafold_db)
download_entire_pdb() (Bio.PDB.PDBList.PDBList method)
download_obsolete_entries() (Bio.PDB.PDBList.PDBList method)
download_pdb_files() (Bio.PDB.PDBList.PDBList method)
draw() (Bio.Graphics.BasicChromosome.Chromosome method)
(Bio.Graphics.BasicChromosome.ChromosomeSegment method)
(Bio.Graphics.BasicChromosome.Organism method)
(Bio.Graphics.BasicChromosome.SpacerSegment method)
(Bio.Graphics.Distribution.BarChartDistribution method)
(Bio.Graphics.Distribution.DistributionPage method)
(Bio.Graphics.Distribution.LineDistribution method)
(Bio.Graphics.GenomeDiagram.Diagram method)
(Bio.Graphics.KGML_vis.KGMLCanvas method)
draw_to_file() (Bio.Graphics.Comparative.ComparativeScatterPlot method)
ds (class in Bio.Sequencing.Ace)
DSSP (class in Bio.PDB.DSSP)
dssp_dict_from_pdb_file() (in module Bio.PDB.DSSP)
duplications() (Bio.Phylo.PhyloXMLIO.Writer method)
E
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)
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)
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)
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)
endIntegerElementHandler() (Bio.Entrez.Parser.DataHandler method)
endNamespaceDeclHandler() (Bio.Entrez.Parser.DataHandler method)
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)
Entity (class in Bio.PDB.Entity)
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)
epost() (in module Bio.Entrez)
ErrorElement (class in Bio.Entrez.Parser)
esearch() (in module Bio.Entrez)
espell() (in module Bio.Entrez)
estimate_params() (Bio.HMM.Trainer.AbstractTrainer method)
esummary() (in module Bio.Entrez)
Events (class in Bio.Phylo.PhyloXML)
events() (Bio.Phylo.PhyloXMLIO.Parser method)
(Bio.Phylo.PhyloXMLIO.Writer method)
ExactPosition (class in Bio.SeqFeature)
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)
export_fasta() (Bio.Nexus.Nexus.Nexus method)
export_phylip() (Bio.Nexus.Nexus.Nexus method)
ExposureCN (class in Bio.PDB.HSExposure)
extend() (Bio.Align.MultipleSeqAlignment method)
(Bio.SCOP.Raf.SeqMap method)
(Bio.Seq.MutableSeq method)
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
FastaBlastIterator (class in Bio.SeqIO.FastaIO)
FastaIterator (class in Bio.SeqIO.FastaIO)
FastaM10Indexer (class in Bio.SearchIO.FastaIO)
FastaM10Iterator() (in module Bio.AlignIO.FastaIO)
FastaM10Parser (class in Bio.SearchIO.FastaIO)
FastaPearsonIterator (class in Bio.SeqIO.FastaIO)
FastaTwoLineIterator (class in Bio.SeqIO.FastaIO)
FastaTwoLineParser() (in module Bio.SeqIO.FastaIO)
FastaTwoLineWriter (class in Bio.SeqIO.FastaIO)
FastaWriter (class in Bio.SeqIO.FastaIO)
FastMMCIFParser (class in Bio.PDB.MMCIFParser)
FastqGeneralIterator() (in module Bio.SeqIO.QualityIO)
FastqIlluminaIterator (class in Bio.SeqIO.QualityIO)
FastqIlluminaWriter (class in Bio.SeqIO.QualityIO)
FastqIteratorAbstractBaseClass (class in Bio.SeqIO.QualityIO)
FastqPhredIterator (class in Bio.SeqIO.QualityIO)
FastqPhredWriter (class in Bio.SeqIO.QualityIO)
FastqSolexaIterator (class in Bio.SeqIO.QualityIO)
FastqSolexaWriter (class in Bio.SeqIO.QualityIO)
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)
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)
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)
fit() (Bio.phenotype.phen_micro.WellRecord method)
(in module Bio.phenotype.pm_fitting)
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)
fmt (Bio.Align.a2m.AlignmentIterator attribute)
(Bio.Align.a2m.AlignmentWriter attribute)
(Bio.Align.bed.AlignmentIterator attribute)
(Bio.Align.bigbed.AlignmentIterator attribute)
(Bio.Align.bigbed.AlignmentWriter attribute)
(Bio.Align.bigmaf.AlignmentIterator attribute)
(Bio.Align.bigmaf.AlignmentWriter attribute)
(Bio.Align.bigpsl.AlignmentIterator attribute)
(Bio.Align.bigpsl.AlignmentWriter attribute)
(Bio.Align.chain.AlignmentIterator attribute)
(Bio.Align.chain.AlignmentWriter 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.SeqIO.AlignmentSequenceIterator property)
fmt_() (in module Bio.Blast.NCBIXML)
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.chain.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)
Fragment (class in Bio.PDB.FragmentMapper)
FragmentMapper (class in Bio.PDB.FragmentMapper)
frequencies (Bio.Align.Alignment property)
FrequencyPositionMatrix (class in Bio.motifs.matrix)
from_bytes() (Bio.Align.bigbed.AutoSQLTable class method)
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.Align.bigbed.AutoSQLTable class method)
(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)
full_string (Bio.SeqIO.QualityIO.InvalidCharError attribute)
full_translate() (Bio.codonalign.codonseq.CodonSeq method)
G
gafbyproteiniterator() (in module Bio.UniProt.GOA)
gafiterator() (in module Bio.UniProt.GOA)
gaponly() (Bio.Nexus.Nexus.Nexus method)
gaps (Bio.Align.AlignmentCounts property)
GB_BASE_INDENT (Bio.GenBank.Record.Record attribute)
GB_FEATURE_INDENT (Bio.GenBank.Record.Record attribute)
GB_FEATURE_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute)
GB_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute)
GB_LINE_LENGTH (Bio.GenBank.Record.Record attribute)
GB_OTHER_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute)
GB_SEQUENCE_INDENT (Bio.GenBank.Record.Record attribute)
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)
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)
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)
Generic_dbutils (class in BioSQL.DBUtils)
GenericPositionMatrix (class in Bio.motifs.matrix)
genes (Bio.KEGG.KGML.KGML_pathway.Pathway 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_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_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_feature() (Bio.Graphics.GenomeDiagram.Feature method)
get_features() (Bio.Graphics.GenomeDiagram.FeatureSet 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_graphs() (Bio.Graphics.GenomeDiagram.GraphSet method)
get_guide_coord_from_structure() (Bio.PDB.cealign.CEAligner method)
get_header() (Bio.PDB.PDBParser.PDBParser 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.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_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_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_predictions() (in module Bio.PDB.alphafold_db)
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_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.SVDSuperimposer.SVDSuperimposer method)
get_rotran() (Bio.PDB.qcprot.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_structural_models_for() (in module Bio.PDB.alphafold_db)
get_structure() (Bio.PDB.binary_cif.BinaryCIFParser method)
(Bio.PDB.MMCIFParser.FastMMCIFParser method)
(Bio.PDB.MMCIFParser.MMCIFParser method)
(Bio.PDB.mmtf.MMTFParser static method)
(Bio.PDB.PDBMLParser.PDBMLParser 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.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)
Gfa1Iterator (class in Bio.SeqIO.GfaIO)
Gfa2Iterator (class in Bio.SeqIO.GfaIO)
global_dtd_dir (Bio.Entrez.Parser.DataHandler attribute)
global_xsd_dir (Bio.Entrez.Parser.DataHandler attribute)
gly_Cbeta (Bio.PDB.internal_coords.IC_Residue attribute)
gompertz() (in module Bio.phenotype.pm_fitting)
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)
gs_mapping (Bio.Align.stockholm.AlignmentIterator attribute)
(Bio.Align.stockholm.AlignmentWriter attribute)
guess_lag() (in module Bio.phenotype.pm_fitting)
guess_plateau() (in module Bio.phenotype.pm_fitting)
H
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)
hashedDomainsByEv() (Bio.SCOP.Astral method)
hashedDomainsById() (Bio.SCOP.Astral method)
Header (class in Bio.Blast.NCBIXML)
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)
Hhsuite2TextParser (class in Bio.SearchIO.HHsuiteIO.hhsuite2_text)
HiddenMarkovModel (class in Bio.HMM.MarkovModel)
Hit (class in Bio.Blast)
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)
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)
HSExposureCA (class in Bio.PDB.HSExposure)
HSExposureCB (class in Bio.PDB.HSExposure)
HSP (class in Bio.Blast)
(class in Bio.Blast.NCBIXML)
I
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 property)
identity_match (class in Bio.pairwise2)
IgIterator (class in Bio.SeqIO.IgIO)
ImgtIterator (class in Bio.SeqIO.InsdcIO)
ImgtWriter (class in Bio.SeqIO.InsdcIO)
Indent (Bio.Restriction.PrintFormat.PrintFormat attribute)
index (Bio.SeqIO.QualityIO.InvalidCharError attribute)
Index (class in Bio.SCOP.Cla)
index() (Bio.Blast.Record method)
(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_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)
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)
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)
insertions (Bio.Align.AlignmentCounts property)
instability_index() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
Instance (class in Bio.motifs.meme)
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_deletions (Bio.Align.AlignmentCounts property)
INTERNAL_FEATURE_FORMAT (Bio.GenBank.Record.Record attribute)
INTERNAL_FORMAT (Bio.GenBank.Record.Record attribute)
internal_gaps (Bio.Align.AlignmentCounts property)
internal_insertions (Bio.Align.AlignmentCounts property)
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)
InvalidCharError
inverse_indices (Bio.Align.Alignment property)
invert() (Bio.Nexus.Nexus.Nexus method)
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)
isupper() (Bio.Seq.SequenceDataAbstractBaseClass method)
(Bio.SeqRecord.SeqRecord method)
items() (Bio.Align.substitution_matrices.Array method)
(Bio.Phylo.PhyloXML.Events method)
(BioSQL.BioSeqDatabase.BioSeqDatabase method)
(BioSQL.BioSeqDatabase.DBServer method)
Iterator (class in Bio.GenBank)
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)
K
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.Blast.Record 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)
kmedoids() (in module Bio.Cluster)
KnownStateTrainer (class in Bio.HMM.Trainer)
L
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)
lcc_mult() (in module Bio.SeqUtils.lcc)
lcc_simp() (in module Bio.SeqUtils.lcc)
left_deletions (Bio.Align.AlignmentCounts property)
left_gaps (Bio.Align.AlignmentCounts property)
left_insertions (Bio.Align.AlignmentCounts property)
left_multiply() (Bio.PDB.vectors.Vector method)
len12 (Bio.PDB.internal_coords.Hedron property)
len23 (Bio.PDB.internal_coords.Hedron property)
length (Bio.Align.Alignment 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)
level (Bio.PDB.Entity.Entity attribute)
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)
load() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
(in module Bio.Align.substitution_matrices)
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)
Location (class in Bio.SeqFeature)
location() (Bio.Phylo.PhyloXMLIO.Writer method)
LocationParserError
log_likelihood() (Bio.HMM.Trainer.AbstractTrainer method)
log_odds() (Bio.motifs.matrix.PositionWeightMatrix method)
LogDPAlgorithms (class in Bio.HMM.DynamicProgramming)
logistic() (in module Bio.phenotype.pm_fitting)
long() (Bio.Phylo.PhyloXMLIO.Writer method)
lookup() (BioSQL.BioSeqDatabase.BioSeqDatabase method)
losses() (Bio.Phylo.PhyloXMLIO.Writer method)
lower() (Bio.Seq.SequenceDataAbstractBaseClass method)
(Bio.SeqRecord.SeqRecord method)
lstrip() (Bio.Seq.SequenceDataAbstractBaseClass method)
M
m2rotaxis() (in module Bio.PDB.vectors)
MafIndex (class in Bio.AlignIO.MafIO)
MafIterator() (in module Bio.AlignIO.MafIO)
MafWriter (class in Bio.AlignIO.MafIO)
majority_consensus() (in module Bio.Phylo.Consensus)
make_back_table() (in module Bio.Data.CodonTable)
make_dssp_dict() (in module Bio.PDB.DSSP)
make_extended() (Bio.PDB.internal_coords.IC_Chain method)
make_format() (Bio.Restriction.PrintFormat.PrintFormat method)
make_table() (in module Bio.SeqUtils.MeltingTemp)
make_virtual_offset() (in module Bio.bgzf)
map() (Bio.Align.Alignment method)
mapall() (Bio.Align.Alignment method)
maps (Bio.KEGG.KGML.KGML_pathway.Pathway property)
MarkovModelBuilder (class in Bio.HMM.MarkovModel)
mask (Bio.motifs.Motif property)
MATCH (Bio.Align.tabular.State attribute)
matches() (in module Bio.Phylo.NeXMLIO)
MauveIterator (class in Bio.AlignIO.MauveIO)
MauveWriter (class in Bio.AlignIO.MauveIO)
max (Bio.motifs.matrix.PositionSpecificScoringMatrix property)
maximum() (Bio.Phylo.PhyloXMLIO.Writer method)
MaxPeptideBond (Bio.PDB.internal_coords.IC_Chain attribute)
MaxSize (Bio.Restriction.PrintFormat.PrintFormat attribute)
mean() (Bio.Graphics.GenomeDiagram.GraphData method)
(Bio.motifs.matrix.PositionSpecificScoringMatrix method)
merge_with_support() (Bio.Nexus.Trees.Tree method)
methods (Bio.Phylo.TreeConstruction.DistanceTreeConstructor attribute)
min (Bio.motifs.matrix.PositionSpecificScoringMatrix property)
min_dist() (in module Bio.PDB.ResidueDepth)
minimum() (Bio.Phylo.PhyloXMLIO.Writer method)
mismatches (Bio.Align.AlignmentCounts property)
MissingAtomError
MissingExternalDependencyError
MissingPythonDependencyError
mktest() (in module Bio.Align.analysis)
(in module Bio.codonalign.codonalignment)
ml_estimator() (Bio.HMM.Trainer.AbstractTrainer method)
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.bigbed.AlignmentIterator attribute)
(Bio.Align.bigbed.AlignmentWriter attribute)
(Bio.Align.bigmaf.AlignmentIterator attribute)
(Bio.Align.interfaces.AlignmentIterator attribute)
(Bio.Align.interfaces.AlignmentWriter attribute)
Model (class in Bio.PDB.Model)
models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute)
modes (Bio.SeqIO.AbiIO.AbiIterator attribute)
(Bio.SeqIO.AceIO.AceIterator attribute)
(Bio.SeqIO.AlignmentSequenceIterator attribute)
(Bio.SeqIO.AlignmentSequenceWriter attribute)
(Bio.SeqIO.FastaIO.FastaBlastIterator attribute)
(Bio.SeqIO.FastaIO.FastaIterator attribute)
(Bio.SeqIO.FastaIO.FastaPearsonIterator attribute)
(Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute)
(Bio.SeqIO.FastaIO.FastaWriter attribute)
(Bio.SeqIO.GckIO.GckIterator attribute)
(Bio.SeqIO.GfaIO.Gfa1Iterator attribute)
(Bio.SeqIO.GfaIO.Gfa2Iterator 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 property)
(Bio.SeqIO.Interfaces.SequenceWriter property)
(Bio.SeqIO.NibIO.NibIterator attribute)
(Bio.SeqIO.NibIO.NibWriter attribute)
(Bio.SeqIO.PdbIO.CifAtomIterator attribute)
(Bio.SeqIO.PdbIO.CifSeqresIterator attribute)
(Bio.SeqIO.PdbIO.PdbAtomIterator attribute)
(Bio.SeqIO.PdbIO.PdbSeqresIterator attribute)
(Bio.SeqIO.PhdIO.PhdIterator attribute)
(Bio.SeqIO.PhdIO.PhdWriter attribute)
(Bio.SeqIO.PirIO.PirIterator attribute)
(Bio.SeqIO.PirIO.PirWriter attribute)
(Bio.SeqIO.QualityIO.FastqIlluminaWriter attribute)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute)
(Bio.SeqIO.QualityIO.FastqPhredWriter attribute)
(Bio.SeqIO.QualityIO.FastqSolexaWriter attribute)
(Bio.SeqIO.QualityIO.QualPhredIterator attribute)
(Bio.SeqIO.QualityIO.QualPhredWriter attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter attribute)
(Bio.SeqIO.SffIO.SffIterator attribute)
(Bio.SeqIO.SffIO.SffWriter attribute)
(Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute)
(Bio.SeqIO.SwissIO.SwissIterator attribute)
(Bio.SeqIO.TabIO.TabIterator attribute)
(Bio.SeqIO.TabIO.TabWriter attribute)
(Bio.SeqIO.TwoBitIO.TwoBitIterator attribute)
(Bio.SeqIO.UniprotIO.UniprotIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaIterator attribute)
(Bio.SeqIO.XdnaIO.XdnaWriter attribute)
modify() (Bio.motifs.thresholds.ScoreDistribution method)
module
Bio
Bio.Affy
Bio.Affy.CelFile
Bio.Align
Bio.Align.a2m
Bio.Align.AlignInfo
Bio.Align.analysis
Bio.Align.bed
Bio.Align.bigbed
Bio.Align.bigmaf
Bio.Align.bigpsl
Bio.Align.chain
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.bgzf
Bio.Blast
Bio.Blast.NCBIWWW
Bio.Blast.NCBIXML
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.Emboss
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.Medline
Bio.motifs
Bio.motifs.alignace
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.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.alphafold_db
Bio.PDB.Atom
Bio.PDB.binary_cif
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.PDBMLParser
Bio.PDB.PDBParser
Bio.PDB.PICIO
Bio.PDB.Polypeptide
Bio.PDB.PSEA
Bio.PDB.qcprot
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.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.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_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.GfaIO
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.Phd
Bio.SeqUtils
Bio.SeqUtils.CheckSum
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
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)
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)
MsfIterator (class in Bio.AlignIO.MsfIO)
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_value_keys (Bio.motifs.transfac.Motif attribute)
MultipleAlignment (class in Bio.Blast.NCBIXML)
MultipleSeqAlignment (class in Bio.Align)
MutableSeq (class in Bio.Seq)
Mysql_dbutils (class in BioSQL.DBUtils)
MysqlConnectorAdaptor (class in BioSQL.BioSeqDatabase)
N
NACCESS (class in Bio.PDB.NACCESS)
NACCESS_atomic (class in Bio.PDB.NACCESS)
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)
name() (Bio.Phylo.PhyloXMLIO.Writer method)
NameWidth (Bio.Restriction.PrintFormat.PrintFormat attribute)
NCBICodonTable (class in Bio.Data.CodonTable)
NCBICodonTableDNA (class in Bio.Data.CodonTable)
NCBICodonTableRNA (class in Bio.Data.CodonTable)
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
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.TreeConstruction.DistanceTreeConstructor method)
NNITreeSearcher (class in Bio.Phylo.TreeConstruction)
no_altloc (Bio.PDB.internal_coords.IC_Residue attribute)
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)
NONE (Bio.Align.tabular.State attribute)
NoneElement (class in Bio.Entrez.Parser)
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)
NotXMLError
,
[1]
nt_search() (in module Bio.SeqUtils)
nucleotide_alphabet (Bio.Data.CodonTable.NCBICodonTable attribute)
(Bio.Data.CodonTable.NCBICodonTableDNA attribute)
(Bio.Data.CodonTable.NCBICodonTableRNA attribute)
number (Bio.KEGG.KGML.KGML_pathway.Pathway property)
O
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)
one_to_index() (in module Bio.PDB.Polypeptide)
OneOfPosition (class in Bio.SeqFeature)
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)
optimize() (Bio.SeqUtils.CodonAdaptationIndex method)
OrderedListElement (class in Bio.Entrez.Parser)
Organism (class in Bio.Graphics.BasicChromosome)
orthologs (Bio.KEGG.KGML.KGML_pathway.Pathway 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)
out_block() (in module Bio.Geo.Record)
OutputRecord (class in Bio.Emboss.PrimerSearch)
P
PairedFastaQualIterator() (in module Bio.SeqIO.QualityIO)
PairwiseAligner (class in Bio.Align)
PairwiseAlignments (class in Bio.Align)
ParallelAssembleResidues (Bio.PDB.internal_coords.IC_Chain attribute)
Parameters (class in Bio.Blast.NCBIXML)
parent (Bio.PDB.Entity.Entity attribute)
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)
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)
(in module Bio.Align)
(in module Bio.AlignIO)
(in module Bio.Blast)
(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)
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_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_pdb_header() (in module Bio.PDB.parse_pdb_header)
parse_preamble() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
parse_printed_alignment() (Bio.Align.Alignment class method)
parse_qresult() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
parse_records() (Bio.GenBank.Scanner.InsdcScanner method)
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)
ParserError
ParserFailureError
ParsimonyScorer (class in Bio.Phylo.TreeConstruction)
ParsimonyTreeConstructor (class in Bio.Phylo.TreeConstruction)
parts (Bio.SeqFeature.SimpleLocation property)
Pathway (class in Bio.KEGG.KGML.KGML_pathway)
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 (class in Bio.SeqIO.PdbIO)
PDBConstructionException
PDBConstructionWarning
PDBException
PDBIO (class in Bio.PDB.PDBIO)
PDBIOException
PDBList (class in Bio.PDB.PDBList)
PDBMLParser (class in Bio.PDB.PDBMLParser)
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)
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 (class in Bio.SeqIO.PhdIO)
PhdWriter (class in Bio.SeqIO.PhdIO)
phred_quality_from_solexa() (in module Bio.SeqIO.QualityIO)
PhylipIterator (class in Bio.AlignIO.PhylipIO)
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
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)
PirIterator (class in Bio.SeqIO.PirIO)
PirWriter (class in Bio.SeqIO.PirIO)
PlateRecord (class in Bio.phenotype.phen_micro)
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)
Position (class in Bio.SeqFeature)
POSITION_PADDING (Bio.SeqIO.InsdcIO.EmblWriter attribute)
PositionSpecificScoringMatrix (class in Bio.motifs.matrix)
PositionWeightMatrix (class in Bio.motifs.matrix)
positives (Bio.Align.AlignmentCounts property)
PPBuilder (class in Bio.PDB.Polypeptide)
predictNOE() (in module Bio.NMR.NOEtools)
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)
Primers (class in Bio.Emboss.Primer3)
print_as() (Bio.Restriction.PrintFormat.PrintFormat method)
print_matrix() (in module Bio.pairwise2)
print_options() (Bio.Phylo.PAML.codeml.Codeml method)
print_that() (Bio.Restriction.PrintFormat.PrintFormat method)
PrintFormat (class in Bio.Restriction.PrintFormat)
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)
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_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)
pseudocounts (Bio.motifs.Motif property)
PSIBlast (class in Bio.Blast.NCBIXML)
pssm (Bio.motifs.Motif property)
Psycopg2_dbutils (class in BioSQL.DBUtils)
push_back() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
pwm (Bio.motifs.Motif property)
Q
q_key (Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass property)
(Bio.SeqIO.QualityIO.FastqPhredIterator attribute)
(Bio.SeqIO.QualityIO.FastqSolexaIterator attribute)
q_mapping (Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute)
(Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass property)
(Bio.SeqIO.QualityIO.FastqPhredIterator attribute)
(Bio.SeqIO.QualityIO.FastqSolexaIterator attribute)
qa (class in Bio.Sequencing.Ace)
qblast() (in module Bio.Blast)
(in module Bio.Blast.NCBIWWW)
qcp() (in module Bio.PDB.qcprot)
QCPSuperimposer (class in Bio.PDB.qcprot)
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)
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)
QualPhredIterator (class in Bio.SeqIO.QualityIO)
QualPhredWriter (class in Bio.SeqIO.QualityIO)
quartiles() (Bio.Graphics.GenomeDiagram.GraphData method)
query (Bio.Align.Alignment property)
query_coverage() (Bio.Compass.Record method)
QUERY_GAP (Bio.Align.tabular.State attribute)
quotestrip() (in module Bio.Nexus.Nexus)
qUri() (in module Bio.Phylo.CDAOIO)
(in module Bio.Phylo.NeXMLIO)
R
r (Bio.SeqIO.QualityIO.InvalidCharError attribute)
rak() (Bio.PDB.internal_coords.IC_Residue method)
randomize() (Bio.Nexus.Trees.Tree method)
randomized() (Bio.Phylo.BaseTree.Tree class method)
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)
raw() (Bio.Nexus.StandardData.StandardData method)
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)
(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_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_header_fmt (Bio.SeqIO.SffIO.SffIterator attribute)
read_header_size (Bio.SeqIO.SffIO.SffIterator attribute)
read_next() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method)
read_PIC() (in module Bio.PDB.PICIO)
read_PIC_seq() (in module Bio.PDB.PICIO)
readline() (Bio.bgzf.BgzfReader method)
ReadRocheXmlManifest() (in module Bio.SeqIO.SffIO)
Reads (class in Bio.Sequencing.Ace)
Record (class in Bio.Affy.CelFile)
(class in Bio.Blast)
(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)
RecordParser (class in Bio.GenBank)
Records (class in Bio.Blast)
red() (Bio.Phylo.PhyloXMLIO.Writer method)
ref (Bio.SeqFeature.CompoundLocation property)
ref_db (Bio.SeqFeature.CompoundLocation 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)
refmat() (in module Bio.PDB.vectors)
register_ncbi_table() (in module Bio.Data.CodonTable)
Relation (class in Bio.KEGG.KGML.KGML_pathway)
relations (Bio.KEGG.KGML.KGML_pathway.Pathway property)
relative_entropy (Bio.motifs.Motif property)
RelaxedPhylipIterator (class in Bio.AlignIO.PhylipIO)
RelaxedPhylipWriter (class in Bio.AlignIO.PhylipIO)
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)
removeprefix() (Bio.Seq.SequenceDataAbstractBaseClass method)
removesuffix() (Bio.Seq.SequenceDataAbstractBaseClass method)
renumber_tracks() (Bio.Graphics.GenomeDiagram.Diagram method)
replace() (Bio.Seq.SequenceDataAbstractBaseClass method)
replace_entry() (in module Bio.NMR.xpktools)
report_IC() (in module Bio.PDB.ic_rebuild)
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)
Residues (class in Bio.SCOP.Residues)
rest() (Bio.Nexus.Nexus.CharBuffer method)
retrieve_assembly_file() (Bio.PDB.PDBList.PDBList method)
retrieve_pdb_file() (Bio.PDB.PDBList.PDBList method)
reverse() (Bio.Pathway.Reaction method)
(Bio.Seq.MutableSeq method)
reverse_complement() (Bio.Align.Alignment 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)
rewind() (Bio.Align.Alignments method)
(Bio.Align.AlignmentsAbstractBaseClass method)
(Bio.Align.interfaces.AlignmentIterator method)
(Bio.Align.PairwiseAlignments method)
rfind() (Bio.Seq.SequenceDataAbstractBaseClass method)
richards() (in module Bio.phenotype.pm_fitting)
right_deletions (Bio.Align.AlignmentCounts property)
right_gaps (Bio.Align.AlignmentCounts property)
right_insertions (Bio.Align.AlignmentCounts property)
right_multiply() (Bio.PDB.vectors.Vector method)
rindex() (Bio.Seq.SequenceDataAbstractBaseClass method)
rollback() (BioSQL.BioSeqDatabase.Adaptor method)
(BioSQL.BioSeqDatabase.DBServer method)
root (Bio.Phylo.BaseTree.Clade 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.NCBIXML)
rsplit() (Bio.Seq.SequenceDataAbstractBaseClass method)
rstrip() (Bio.Seq.SequenceDataAbstractBaseClass method)
rt (class in Bio.Sequencing.Ace)
run() (Bio.PDB.qcprot.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_naccess() (in module Bio.PDB.NACCESS)
run_psea() (in module Bio.PDB.PSEA)
S
safename() (in module Bio.Nexus.Nexus)
salt_correction() (in module Bio.SeqUtils.MeltingTemp)
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)
save_dtd_file() (Bio.Entrez.Parser.DataHandler method)
save_xsd_file() (Bio.Entrez.Parser.DataHandler method)
scale_segment_value() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method)
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.pairwise2.Alignment attribute)
score() (Bio.Align.CodonAligner method)
(Bio.Align.PairwiseAligner method)
ScoreDistribution (class in Bio.motifs.thresholds)
Scorer (class in Bio.Phylo.TreeConstruction)
search() (Bio.Align.bigbed.AlignmentIterator method)
(Bio.AlignIO.MafIO.MafIndex 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)
(in module Bio.UniProt)
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)
secondary_structure_fraction() (Bio.SeqUtils.ProtParam.ProteinAnalysis method)
seek() (Bio.bgzf.BgzfReader method)
seek_position() (Bio.PopGen.GenePop.FileParser.FileRecord method)
seekable() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
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)
seqA (Bio.pairwise2.Alignment attribute)
seqB (Bio.pairwise2.Alignment attribute)
SeqFeature (class in Bio.SeqFeature)
SeqMap (class in Bio.SCOP.Raf)
SeqMapIndex (class in Bio.SCOP.Raf)
SeqRecord (class in Bio.SeqRecord)
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)
SequenceWriter (class in Bio.SeqIO.Interfaces)
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.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_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_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)
shape (Bio.Align.Alignment property)
ShrakeRupley (class in Bio.PDB.SASA)
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)
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)
smprint() (Bio.Nexus.Nexus.StepMatrix method)
SnapGeneIterator (class in Bio.SeqIO.SnapGeneIO)
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)
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)
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)
Sqlite_dbutils (class in BioSQL.DBUtils)
ss_to_index() (in module Bio.PDB.DSSP)
StandardData (class in Bio.Nexus.StandardData)
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)
startEntryFieldElementVersion01() (Bio.SeqIO.SeqXmlIO.ContentHandler method)
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)
status_characters (Bio.Align.maf.AlignmentIterator attribute)
std() (Bio.motifs.matrix.PositionSpecificScoringMatrix method)
stdev() (Bio.Graphics.GenomeDiagram.GraphData method)
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.SeqFeature.CompoundLocation property)
(Bio.SeqFeature.SimpleLocation property)
StreamModeError
strict_consensus() (in module Bio.Phylo.Consensus)
strictly_equals() (Bio.PDB.Atom.Atom method)
(Bio.PDB.Entity.DisorderedEntityWrapper method)
(Bio.PDB.Entity.Entity method)
(Bio.PDB.Residue.Residue method)
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)
subcomponent_size() (Bio.Graphics.BasicChromosome.Chromosome method)
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)
sum() (Bio.Nexus.Nexus.StepMatrix method)
sum_branchlength() (Bio.Nexus.Trees.Tree method)
SummaryInfo (class in Bio.Align.AlignInfo)
Superimposer (class in Bio.PDB.Superimposer)
SVDSuperimposer (class in Bio.SVDSuperimposer)
SwissIterator (class in Bio.SeqIO.SwissIO)
SwissProtParserError
symbol() (Bio.Phylo.PhyloXMLIO.Writer method)
synonym() (Bio.Phylo.PhyloXMLIO.Writer method)
System (class in Bio.Pathway)
T
TabIterator (class in Bio.SeqIO.TabIO)
TabWriter (class in Bio.SeqIO.TabIO)
target (Bio.Align.Alignment property)
TARGET_GAP (Bio.Align.tabular.State attribute)
taxonomy (Bio.Phylo.PhyloXML.Clade property)
Taxonomy (class in Bio.Phylo.PhyloXML)
taxonomy() (Bio.Phylo.PhyloXMLIO.Writer method)
tell() (Bio.bgzf.BgzfReader method)
(Bio.bgzf.BgzfWriter method)
TelomereSegment (class in Bio.Graphics.BasicChromosome)
terminal_gap_to_missing() (Bio.Nexus.Nexus.Nexus method)
three_to_index() (in module Bio.PDB.Polypeptide)
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)
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.NCBIXML.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)
(Bio.SeqIO.FastaIO.FastaTwoLineWriter class method)
(Bio.SeqIO.FastaIO.FastaWriter class method)
(Bio.SeqIO.Interfaces.SequenceWriter class method)
(Bio.SeqIO.QualityIO.FastqIlluminaWriter class method)
(Bio.SeqIO.QualityIO.FastqPhredWriter class method)
(Bio.SeqIO.QualityIO.FastqSolexaWriter class method)
(Bio.SeqIO.QualityIO.QualPhredWriter class method)
(Bio.SeqIO.TabIO.TabWriter class 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)
toSeq() (Bio.codonalign.codonseq.CodonSeq method)
total_branch_length() (Bio.Phylo.BaseTree.TreeMixin method)
trace() (Bio.Nexus.Nodes.Chain method)
(Bio.Phylo.BaseTree.TreeMixin method)
Track (class in Bio.Graphics.GenomeDiagram)
train() (Bio.HMM.Trainer.BaumWelchTrainer method)
(Bio.HMM.Trainer.KnownStateTrainer method)
TrainingSequence (class in Bio.HMM.Trainer)
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.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)
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)
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)
TreeSearcher (class in Bio.Phylo.TreeConstruction)
TwoBitIterator (class in Bio.SeqIO.TwoBitIO)
type() (Bio.Phylo.PhyloXMLIO.Writer method)
types (Bio.Phylo.PhyloXML.Sequence attribute)
U
UncertainPosition (class in Bio.SeqFeature)
UndefinedSequenceError
unfold_entities() (in module Bio.PDB.Selection)
ungap() (Bio.codonalign.codonseq.CodonSeq method)
UniprotIterator (class in 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)
V
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)
Vector (class in Bio.PDB.vectors)
vector_to_axis() (in module Bio.PDB.vectors)
version (Bio.motifs.jaspar.Motif property)
version() (in module Bio.PDB.DSSP)
viterbi() (Bio.HMM.MarkovModel.HiddenMarkovModel method)
W
wa (class in Bio.Sequencing.Ace)
weblogo() (Bio.motifs.Motif method)
weighted_stepmatrix() (Bio.Nexus.Nexus.Nexus method)
weighting() (Bio.Nexus.Nexus.StepMatrix method)
WellRecord (class in Bio.phenotype.phen_micro)
width (Bio.KEGG.KGML.KGML_pathway.Graphics property)
width() (Bio.Phylo.PhyloXMLIO.Writer method)
WithinPosition (class in Bio.SeqFeature)
wr (class in Bio.Sequencing.Ace)
write() (Bio.Align.interfaces.AlignmentWriter method)
(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.Blast)
(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.bigbed.AlignmentWriter method)
(Bio.Align.interfaces.AlignmentWriter method)
(Bio.Align.nexus.AlignmentWriter method)
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.bigbed.AlignmentWriter method)
(Bio.Align.bigmaf.AlignmentWriter method)
(Bio.Align.bigpsl.AlignmentWriter method)
(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)
write_footer() (Bio.Align.exonerate.AlignmentWriter method)
(Bio.Align.interfaces.AlignmentWriter method)
(Bio.AlignIO.Interfaces.SequentialAlignmentWriter 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.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.AlignmentSequenceWriter method)
(Bio.SeqIO.Interfaces.SequenceWriter method)
(Bio.SeqIO.NibIO.NibWriter method)
(Bio.SeqIO.SeqXmlIO.SeqXmlWriter method)
(Bio.SeqIO.SffIO.SffWriter method)
(Bio.SeqIO.XdnaIO.XdnaWriter method)
write_SCAD() (in module Bio.PDB.SCADIO)
write_single_alignment() (Bio.Align.interfaces.AlignmentWriter method)
write_to_string() (Bio.Graphics.GenomeDiagram.Diagram method)
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)
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
Biopython v: 1.86.dev0
Versions
Previous
Latest
Develop
Biopython Project
Homepage
On GitHub