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]
_
__abs__()
(in
Confidence
)
__package__
(in
Bio.Graphics
)
_gaf20iterator()
(in
Bio.UniProt.GOA
)
__add__()
(in
MultipleSeqAlignment
)
__package__
(in
Bio.HMM.DynamicProgramming
)
_gen_random_array()
(in
Bio.HMM.MarkovModel
)
__add__()
(in
Chain
)
__package__
(in
Bio.HMM.MarkovModel
)
_genbank_convert_fasta()
(in
Bio.SeqIO._convert
)
__add__()
(in
Vector
)
__package__
(in
Bio.HMM.Trainer
)
_GenePopCommandline
(in
Bio.PopGen.GenePop.Controller
)
__add__()
(in
Confidence
)
__package__
(in
Bio.HMM.Utilities
)
_generate_full_id()
(in
Entity
)
__add__()
(in
RestrictionBatch
)
__package__
(in
Bio.HMM
)
_genes()
(in
Record
)
__add__()
(in
RestrictionType
)
__package__
(in
Bio.Index
)
_get_a()
(in
ColorSpiral
)
__add__()
(in
SeqMap
)
__package__
(in
Bio.KDTree.KDTree'
)
_get_aa_regex()
(in
Bio.codonalign
)
__add__()
(in
MutableSeq
)
__package__
(in
Bio.KDTree._CKDTree
)
_get_all_letters()
(in
SummaryInfo
)
__add__()
(in
Seq
)
__package__
(in
Bio.KDTree
)
_get_aln_slice_coords()
(in
Bio.SearchIO.FastaIO
)
__add__()
(in
UnknownSeq
)
__package__
(in
Bio.KEGG.Compound
)
_get_annotation_str()
(in
_InsdcWriter
)
__add__()
(in
CompoundLocation
)
__package__
(in
Bio.KEGG.Enzyme
)
_get_atom_line()
(in
PDBIO
)
__add__()
(in
FeatureLocation
)
__package__
(in
Bio.KEGG.Gene
)
_get_atom_radius()
(in
Bio.PDB.ResidueDepth'
)
__add__()
(in
SeqRecord
)
__package__
(in
Bio.KEGG.KGML.KGML_parser
)
_get_attribute_value()
(in
Bio.SeqIO.SnapGeneIO
)
__add__()
(in
SeqMat
)
__package__
(in
Bio.KEGG.KGML.KGML_pathway
)
_get_b()
(in
ColorSpiral
)
__add__()
(in
CodonAlignment
)
__package__
(in
Bio.KEGG.KGML
)
_get_base_alphabet()
(in
Bio.Alphabet
)
__add__()
(in
PlateRecord
)
__package__
(in
Bio.KEGG.Map
)
_get_base_letters()
(in
SummaryInfo
)
__add__()
(in
WellRecord
)
__package__
(in
Bio.KEGG.REST
)
_get_base_replacements()
(in
SummaryInfo
)
__add__()
(in
DBSeq
)
__package__
(in
Bio.KEGG
)
_get_bioentry_dbxref()
(in
DatabaseLoader
)
__add_compounds()
(in
KGMLCanvas
)
__package__
(in
Bio.LogisticRegression
)
_get_block_coords()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__add_genes()
(in
KGMLCanvas
)
__package__
(in
Bio.MarkovModel
)
_get_blocks()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__add_graphics()
(in
KGMLCanvas
)
__package__
(in
Bio.MaxEntropy
)
_get_cb()
(in
HSExposureCA
)
__add_labels()
(in
KGMLCanvas
)
__package__
(in
Bio.Medline
)
_get_cb()
(in
HSExposureCB
)
__add_maps()
(in
KGMLCanvas
)
__package__
(in
Bio.NMR.NOEtools
)
_get_cb()
(in
_AbstractHSExposure
)
__add_orthologs()
(in
KGMLCanvas
)
__package__
(in
Bio.NMR
)
_get_child_as()
(in
Bio.Phylo.PhyloXMLIO
)
__add_reaction_entries()
(in
KGMLCanvas
)
__package__
(in
Bio.NMR.xpktools
)
_get_child_text()
(in
Bio.Phylo.PhyloXMLIO
)
__add_relations()
(in
KGMLCanvas
)
__package__
(in
Bio.NaiveBayes
)
_get_child_value()
(in
Bio.SeqIO.SnapGeneIO
)
__and__()
(in
_BitString
)
__package__
(in
Bio.Nexus.Nexus
)
_get_children_as()
(in
Bio.Phylo.PhyloXMLIO
)
__array_finalize__()
(in
Array
)
__package__
(in
Bio.Nexus.Nodes
)
_get_children_text()
(in
Bio.Phylo.PhyloXMLIO
)
__array_prepare__()
(in
Array
)
__package__
(in
Bio.Nexus.StandardData
)
_get_codon2codon_matrix()
(in
Bio.codonalign.codonalignment
)
__array_ufunc__()
(in
Array
)
__package__
(in
Bio.Nexus.Trees
)
_get_codon_fold()
(in
Bio.codonalign.codonseq
)
__array_wrap__()
(in
Array
)
__package__
(in
Bio.Nexus
)
_get_codon_list()
(in
Bio.codonalign.codonseq
)
__bool__()
(in
Clade
)
__package__
(in
Bio.Nexus.cnexus
)
_get_codon_rec()
(in
Bio.codonalign
)
__bool__()
(in
Hit
)
__package__
(in
Bio.PDB.AbstractPropertyMap
)
_get_color()
(in
Clade
)
__bool__()
(in
HSP
)
__package__
(in
Bio.PDB.Atom
)
_get_cols()
(in
Bio.SearchIO._legacy.NCBIStandalone
)
__bool__()
(in
QueryResult
)
__package__
(in
Bio.PDB.Chain
)
_get_column_info_content()
(in
SummaryInfo
)
__bool__()
(in
SeqFeature
)
__package__
(in
Bio.PDB.DSSP'
)
_get_command_lines()
(in
Bio.Nexus.Nexus
)
__bool__()
(in
SeqRecord
)
__package__
(in
Bio.PDB.Dice
)
_get_comment()
(in
Bio.Phylo.NewickIO
)
__call__()
(in
AbstractCommandline
)
__package__
(in
Bio.PDB.Entity
)
_get_confidence()
(in
Clade
)
__call__()
(in
affine_penalty
)
__package__
(in
Bio.PDB.FragmentMapper'
)
_get_confidence()
(in
Phylogeny
)
__call__()
(in
dictionary_match
)
__package__
(in
Bio.PDB.HSExposure
)
_get_convert_formats()
(in
Bio.TogoWS
)
__call__()
(in
identity_match
)
__package__
(in
Bio.PDB.MMCIF2Dict
)
_get_coords()
(in
HSP
)
__check_data()
(in
Bio.Cluster
)
__package__
(in
Bio.PDB.MMCIFParser'
)
_get_coords()
(in
Bio.Wise.dnal
)
__check_distancematrix()
(in
Bio.Cluster
)
__package__
(in
Bio.PDB.Model
)
_get_data_division()
(in
EmblWriter
)
__check_existing_db()
(in
MafIndex
)
__package__
(in
Bio.PDB.NACCESS
)
_get_data_division()
(in
GenBankWriter
)
__check_index()
(in
Bio.Cluster
)
__package__
(in
Bio.PDB.NeighborSearch'
)
_get_date()
(in
GenBankWriter
)
__check_initialid()
(in
Bio.Cluster
)
__package__
(in
Bio.PDB.PDBExceptions
)
_get_dbxref_id()
(in
DatabaseLoader
)
__check_mask()
(in
Bio.Cluster
)
__package__
(in
Bio.PDB.PDBIO'
)
_get_entry_dbs()
(in
Bio.TogoWS
)
__check_weight()
(in
Bio.Cluster
)
__package__
(in
Bio.PDB.PDBList'
)
_get_entry_fields()
(in
Bio.TogoWS
)
__cmp__()
(in
PairwiseAlignment
)
__package__
(in
Bio.PDB.PDBParser'
)
_get_entry_formats()
(in
Bio.TogoWS
)
__contains__()
(in
Array
)
__package__
(in
Bio.PDB.PSEA
)
_get_fields()
(in
Bio.TogoWS
)
__contains__()
(in
Chain
)
__package__
(in
Bio.PDB.Polypeptide
)
_get_frag_frame()
(in
BlastTabParser
)
__contains__()
(in
Crystal
)
__package__
(in
Bio.PDB.QCPSuperimposer
)
_get_frag_strand()
(in
BlastTabParser
)
__contains__()
(in
AmbiguousForwardTable
)
__package__
(in
Bio.PDB.QCPSuperimposer.qcprotmodule
)
_get_fragments_coord()
(in
Bio.SearchIO.ExonerateIO._base
)
__contains__()
(in
_IndexedSeqFileDict
)
__package__
(in
Bio.PDB.Residue
)
_get_fragments_phase()
(in
Bio.SearchIO.ExonerateIO._base
)
__contains__()
(in
_SQLiteManySeqFilesDict
)
__package__
(in
Bio.PDB.ResidueDepth'
)
_get_gap_char()
(in
SummaryInfo
)
__contains__()
(in
AbstractPropertyMap
)
__package__
(in
Bio.PDB.Selection
)
_get_gly_cb_vector()
(in
_AbstractHSExposure
)
__contains__()
(in
Chain
)
__package__
(in
Bio.PDB.Structure
)
_get_header()
(in
PDBParser
)
__contains__()
(in
DisorderedEntityWrapper
)
__package__
(in
Bio.PDB.StructureAlignment'
)
_get_id()
(in
Chain
)
__contains__()
(in
Entity
)
__package__
(in
Bio.PDB.StructureBuilder
)
_get_id()
(in
BlastTabParser
)
__contains__()
(in
FragmentMapper
)
__package__
(in
Bio.PDB.Superimposer'
)
_get_illumina_quality_str()
(in
Bio.SeqIO.QualityIO
)
__contains__()
(in
Vector
)
__package__
(in
Bio.PDB
)
_get_indices()
(in
Nexus
)
__contains__()
(in
Events
)
__package__
(in
Bio.PDB.kdtrees
)
_get_inter_coords()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__contains__()
(in
RestrictionBatch
)
__package__
(in
Bio.PDB.mmcifio
)
_get_jitter()
(in
ColorSpiral
)
__contains__()
(in
Hit
)
__package__
(in
Bio.PDB.parse_pdb_header'
)
_get_journal()
(in
Bio.PDB.parse_pdb_header'
)
__contains__()
(in
HSP
)
__package__
(in
Bio.PDB.vectors
)
_get_kappa_t()
(in
Bio.codonalign.codonseq
)
__contains__()
(in
QueryResult
)
__package__
(in
Bio.Pathway.Rep.Graph
)
_get_label_asym_id()
(in
MMCIFIO
)
__contains__()
(in
Seq
)
__package__
(in
Bio.Pathway.Rep.MultiGraph
)
_get_letter_freqs()
(in
SummaryInfo
)
__contains__()
(in
CompoundLocation
)
__package__
(in
Bio.Pathway.Rep
)
_get_location_operator()
(in
SeqFeature
)
__contains__()
(in
FeatureLocation
)
__package__
(in
Bio.Pathway
)
_get_meta_data()
(in
StockholmIterator
)
__contains__()
(in
SeqFeature
)
__package__
(in
Bio.Phylo.Applications._Fasttree
)
_get_neighbors()
(in
NNITreeSearcher
)
__contains__()
(in
SeqRecord
)
__package__
(in
Bio.Phylo.Applications._Phyml
)
_get_nexus_block()
(in
Nexus
)
__contains__()
(in
PlateRecord
)
__package__
(in
Bio.Phylo.Applications._Raxml
)
_get_ontology_id()
(in
DatabaseLoader
)
__contains__()
(in
BioSeqDatabase
)
__package__
(in
Bio.Phylo.Applications
)
_get_opts()
(in
GenePopController
)
__contains__()
(in
DBServer
)
__package__
(in
Bio.Phylo.BaseTree
)
_get_parameter()
(in
AbstractCommandline
)
__del__()
(in
_InMemoryIndex
)
__package__
(in
Bio.Phylo.CDAO
)
_get_per_column_annotations()
(in
MultipleSeqAlignment
)
__del__()
(in
_ShelveIndex
)
__package__
(in
Bio.Phylo.Consensus
)
_get_phred_quality()
(in
Bio.SeqIO.QualityIO
)
__del__()
(in
_FileIterator
)
__package__
(in
Bio.Phylo.NeXML
)
_get_pi()
(in
Bio.codonalign.codonseq
)
__del_annotations()
(in
DBSeqRecord
)
__package__
(in
Bio.Phylo.NeXMLIO
)
_get_Q()
(in
Bio.codonalign.codonseq
)
__del_dbxrefs()
(in
DBSeqRecord
)
__package__
(in
Bio.Phylo.Newick
)
_get_raw_qresult()
(in
BlastTabIndexer
)
__del_features()
(in
DBSeqRecord
)
__package__
(in
Bio.Phylo.NewickIO
)
_get_raw_qresult_commented()
(in
BlastTabIndexer
)
__del_seq()
(in
DBSeqRecord
)
__package__
(in
Bio.Phylo.NexusIO
)
_get_read_region()
(in
Bio.SeqIO.SffIO
)
__delitem__()
(in
Chain
)
__package__
(in
Bio.Phylo.PAML
)
_get_read_time()
(in
Bio.SeqIO.SffIO
)
__delitem__()
(in
Crystal
)
__package__
(in
Bio.Phylo.PAML._paml
)
_get_read_xy()
(in
Bio.SeqIO.SffIO
)
__delitem__()
(in
_InMemoryIndex
)
__package__
(in
Bio.Phylo.PAML._parse_baseml
)
_get_record()
(in
MafIndex
)
__delitem__()
(in
Chain
)
__package__
(in
Bio.Phylo.PAML._parse_codeml
)
_get_ref()
(in
SeqFeature
)
__delitem__()
(in
Entity
)
__package__
(in
Bio.Phylo.PAML._parse_yn00
)
_get_ref_db()
(in
SeqFeature
)
__delitem__()
(in
Events
)
__package__
(in
Bio.Phylo.PAML.baseml
)
_get_references()
(in
Bio.PDB.parse_pdb_header'
)
__delitem__()
(in
_Matrix
)
__package__
(in
Bio.Phylo.PAML.chi2
)
_get_row_dict()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__delitem__()
(in
Hit
)
__package__
(in
Bio.Phylo.PAML.codeml
)
_get_sanger_quality_str()
(in
Bio.SeqIO.QualityIO
)
__delitem__()
(in
HSP
)
__package__
(in
Bio.Phylo.PAML.yn00
)
_get_scodon_moves()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__delitem__()
(in
QueryResult
)
__package__
(in
Bio.Phylo.PhyloXML
)
_get_seq_str_and_check_alphabet()
(in
Seq
)
__delitem__()
(in
MutableSeq
)
__package__
(in
Bio.Phylo.PhyloXMLIO
)
_get_seq_string()
(in
SequenceWriter
)
__delitem__()
(in
PlateRecord
)
__package__
(in
Bio.Phylo.TreeConstruction
)
_get_seq_string()
(in
Bio.SeqIO.Interfaces
)
__delitem__()
(in
BioSeqDatabase
)
__package__
(in
Bio.Phylo
)
_get_seqfeature_dbxref()
(in
DatabaseLoader
)
__delitem__()
(in
DBServer
)
__package__
(in
Bio.Phylo._cdao_owl
)
_get_shift_anchor_re()
(in
Bio.codonalign
)
__div__()
(in
Confidence
)
__package__
(in
Bio.Phylo._io
)
_get_solexa_quality_str()
(in
Bio.SeqIO.QualityIO
)
__div__()
(in
RestrictionBatch
)
__package__
(in
Bio.Phylo._utils
)
_get_strand()
(in
HSPFragment
)
__div__()
(in
RestrictionType
)
__package__
(in
Bio.PopGen.GenePop.Controller
)
_get_strand()
(in
CompoundLocation
)
__divmod__()
(in
Confidence
)
__package__
(in
Bio.PopGen.GenePop.EasyController
)
_get_strand()
(in
FeatureLocation
)
__doc__
(in
Node
)
__package__
(in
Bio.PopGen.GenePop.FileParser
)
_get_strand()
(in
SeqFeature
)
__draw_arrow()
(in
KGMLCanvas
)
__package__
(in
Bio.PopGen.GenePop.LargeFileParser
)
_get_string_tag()
(in
Bio.SeqIO.AbiIO
)
__enter__()
(in
UndoHandle
)
__package__
(in
Bio.PopGen.GenePop.Utils
)
_get_subgraph()
(in
Bio.codonalign.codonalignment
)
__enter__()
(in
BgzfReader
)
__package__
(in
Bio.PopGen.GenePop
)
_get_taxon_id()
(in
DatabaseLoader
)
__enter__()
(in
BgzfWriter
)
__package__
(in
Bio.PopGen
)
_get_taxon_id_from_ncbi_lineage()
(in
DatabaseLoader
)
__eq__()
(in
PairwiseAlignment
)
__package__
(in
Bio.Restriction.PrintFormat
)
_get_taxon_id_from_ncbi_taxon_id()
(in
DatabaseLoader
)
__eq__()
(in
Chain
)
__package__
(in
Bio.Restriction.Restriction
)
_get_taxonomy()
(in
Clade
)
__eq__()
(in
Hetero
)
__package__
(in
Bio.Restriction.Restriction_Dictionary
)
_get_term_id()
(in
DatabaseLoader
)
__eq__()
(in
NoneElement
)
__package__
(in
Bio.Restriction
)
_get_topology()
(in
GenBankWriter
)
__eq__()
(in
Atom
)
__package__
(in
Bio.SCOP.Cla
)
_get_TV()
(in
Bio.codonalign.codonseq
)
__eq__()
(in
Entity
)
__package__
(in
Bio.SCOP.Des
)
_get_unique_parent_pairs()
(in
NeighborSearch
)
__eq__()
(in
Reaction
)
__package__
(in
Bio.SCOP.Dom
)
_get_v_final()
(in
ColorSpiral
)
__eq__()
(in
Graph
)
__package__
(in
Bio.SCOP.Hie
)
_get_v_init()
(in
ColorSpiral
)
__eq__()
(in
MultiGraph
)
__package__
(in
Bio.SCOP.Raf
)
_get_values()
(in
Tree
)
__eq__()
(in
Confidence
)
__package__
(in
Bio.SCOP.Residues
)
_getbgcolor()
(in
Graphics
)
__eq__()
(in
FormattedSeq
)
__package__
(in
Bio.SCOP
)
_getcoords()
(in
Graphics
)
__eq__()
(in
RestrictionType
)
__package__
(in
Bio.SVDSuperimposer
)
_getentry1()
(in
Relation
)
__eq__()
(in
MutableSeq
)
__package__
(in
Bio.SearchIO.BlastIO
)
_getentry2()
(in
Relation
)
__eq__()
(in
Seq
)
__package__
(in
Bio.SearchIO.BlastIO.blast_tab
)
_getfgcolor()
(in
Graphics
)
__eq__()
(in
CompoundLocation
)
__package__
(in
Bio.SearchIO.BlastIO.blast_text
)
_getheight()
(in
Graphics
)
__eq__()
(in
FeatureLocation
)
__package__
(in
Bio.SearchIO.BlastIO.blast_xml
)
_getid()
(in
Component
)
__eq__()
(in
Reference
)
__package__
(in
Bio.SearchIO.BlatIO
)
_getid()
(in
Entry
)
__eq__()
(in
SeqRecord
)
__package__
(in
Bio.SearchIO.ExonerateIO
)
_getid()
(in
Reaction
)
__eq__()
(in
Motif
)
__package__
(in
Bio.SearchIO.ExonerateIO._base
)
_getname()
(in
Entry
)
__eq__()
(in
PlateRecord
)
__package__
(in
Bio.SearchIO.ExonerateIO.exonerate_cigar
)
_getname()
(in
Pathway
)
__eq__()
(in
WellRecord
)
__package__
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
_getnames()
(in
Reaction
)
__exit__()
(in
UndoHandle
)
__package__
(in
Bio.SearchIO.ExonerateIO.exonerate_vulgar
)
_getnumber()
(in
Pathway
)
__exit__()
(in
BgzfReader
)
__package__
(in
Bio.SearchIO.FastaIO
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Bio.SearchIO.HmmerIO.hmmer2_text
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Bio.PopGen.GenePop.Controller
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Bio.SearchIO.HmmerIO.hmmer3_domtab
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Bio.SearchIO.HmmerIO.hmmer3_tab
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Bio.SearchIO.HmmerIO.hmmer3_text
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Bio.SearchIO.InterproscanIO.interproscan_xml
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Bio.SearchIO._legacy.ParserSupport
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Bio.Phylo.PhyloXMLIO
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Bio.SearchIO._model
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PDBParser
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ClustalIterator
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SeqRecord
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EmbossIterator
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MsfIterator
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DBSeqRecord
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Bio.SearchIO._utils
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DBSeqRecord
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Bio.Seq
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SequentialPhylipIterator
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DBSeqRecord
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Bio.SeqFeature
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StockholmIterator
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Bio.SeqIO.AbiIO
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Bio.SeqIO.AceIO
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DistanceTreeConstructor
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Bio.SeqIO.GckIO
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HSP
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Bio.SeqIO.IgIO
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HSPFragment
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DisorderedEntityWrapper
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Bio.SeqIO.InsdcIO
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HSPFragment
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Bio.SeqIO.Interfaces
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HSPFragment
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Bio.SeqIO.NibIO
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HSPFragment
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PSSM
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Bio.SeqIO.PdbIO
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HSPFragment
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MultipleSeqAlignment
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Bio.SeqIO.PhdIO
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HSP
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PairwiseAlignments
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Bio.SeqIO.PirIO
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HSP
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Bio.SeqIO.QualityIO
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Bio.SearchIO._model.query
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Bio.SeqIO.SeqXmlIO
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HSP
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Crystal
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Bio.SeqIO.SffIO
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HSPFragment
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Bio.SeqIO.SnapGeneIO
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HSPFragment
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fff_rec
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Bio.SeqIO.SwissIO
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HSP
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Bio.SeqIO.TabIO
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HSPFragment
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Bio.SeqIO.UniprotIO
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HSP
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Diagram
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Bio.SeqIO.XdnaIO
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HSPFragment
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FeatureSet
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Bio.SeqIO
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HSPFragment
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GraphData
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Bio.SeqIO._convert
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HSPFragment
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GraphSet
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Bio.SeqIO._index
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HSPFragment
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Track
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Bio.SeqRecord
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Bio.SearchIO.HmmerIO.hmmer2_text
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Bio.SeqUtils.CheckSum
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Bio.phenotype.phen_micro
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Bio.SeqUtils.CodonUsage
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Bio.SearchIO.HmmerIO.hmmer3_text
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Bio.SeqUtils.CodonUsageIndices
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Bio.SearchIO.HmmerIO.hmmer3_text
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DisorderedEntityWrapper
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Bio.SeqUtils.IsoelectricPoint
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Entity
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Bio.SeqUtils.MeltingTemp
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Bio.SeqIO.SffIO
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FragmentMapper
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Bio.SeqUtils.ProtParam
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Bio.SearchIO.HmmerIO.hmmer2_text
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Vector
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Bio.SeqUtils.ProtParamData
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Bio.SearchIO.FastaIO
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Clade
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Bio.SeqUtils
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Bio.SearchIO._legacy.NCBIStandalone
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Events
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Bio.SeqUtils.lcc
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Bio.PopGen.GenePop.Controller
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Phyloxml
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Bio.Sequencing.Ace
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Bio.PDB.Dice
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Bio.Sequencing.Applications._Novoalign
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Bio.AlignIO.MauveIO
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FormattedSeq
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Bio.Sequencing.Applications
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StockholmIterator
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Bio.Sequencing.Applications._bwa
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Bio.Phylo.BaseTree
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SeqMap
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Bio.Sequencing.Applications._samtools
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MauveIterator
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SeqMapIndex
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Bio.Sequencing.Phd
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Bio.codonalign.chisq
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Hit
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Bio.Sequencing
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Bio.codonalign.chisq
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HSP
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Bio.Statistics
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Bio.MaxEntropy
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HSPFragment
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Bio.Statistics.lowess
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Bio.GenBank.Scanner
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QueryResult
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Bio.SubsMat.FreqTable
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Bio.Phylo.PAML.chi2
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Bio.SubsMat.MatrixInfo
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Bio.Phylo.PhyloXMLIO
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Seq
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Bio.SubsMat
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Bio.GenBank.Record
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UnknownSeq
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Bio.SwissProt.KeyWList
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Bio.SearchIO
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SeqRecord
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Bio.SwissProt
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Bio.SeqIO
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CodonAlignment
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Bio.TogoWS
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ScoreDistribution
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CodonSeq
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Bio.UniGene
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Bio.File
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Bio.UniProt.GOA
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Bio.File
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Bio.UniProt
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Bio.SearchIO
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Record
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Bio.Wise
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Writer
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Bio.Wise.dnal
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Record
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Bio.Wise.psw
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WellRecord
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Bio
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STSLine
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DBSeq
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Bio._py3k
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BioSeqDatabase
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Bio._utils
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Bio.SeqUtils.CheckSum
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DBServer
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Bio.bgzf
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SeqMat
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Bio.codonalign
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DataHandler
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Bio.codonalign.chisq
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Bio.Index
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Bio.codonalign.codonalignment
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Bio.SeqIO.AbiIO
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Bio.codonalign.codonalphabet
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Bio.codonalign.codonseq
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QCPSuperimposer
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Bio.cpairwise2
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NcbimakeblastdbCommandline
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Bio.kNN
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Bio.SeqIO.InsdcIO
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Bio.motifs
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Bio.motifs._pwm
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Bio.SeqIO.InsdcIO
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Bio.motifs.alignace
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Bio.SeqIO.InsdcIO
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Bio.motifs.applications
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DatabaseLoader
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Bio.motifs.applications._xxmotif
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Bio.SeqIO.AbiIO
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Bio.motifs.clusterbuster
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Bio.Phylo.PhyloXMLIO
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Bio.motifs.jaspar
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Bio.motifs.mast
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Atom
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Bio.motifs.matrix
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BioSQL.BioSeqDatabase
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Bio.motifs.meme
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Bio.motifs.minimal
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Bio.Phylo
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Bio.motifs.pfm
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Bio.motifs.thresholds
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CaPPBuilder
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PPBuilder
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Bio.motifs.xms
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Bio.pairwise2
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Bio.Phylo.Applications._Fasttree
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Bio.phenotype
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Bio._py3k
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Bio.phenotype.phen_micro
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JASPAR5
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Bio.phenotype.pm_fitting
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SeqMap
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Bio.trie
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Bio.Phylo.TreeConstruction
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MutableSeq
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Bio.triefind
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Bio.SearchIO.BlatIO
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BioSQL.BioSeq
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PlateRecord
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UnknownSeq
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BioSQL.BioSeqDatabase
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Bio.SearchIO
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DBSeq
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BioSQL.DBUtils
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BioSQL.Loader
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Bio.SeqUtils.MeltingTemp
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BioSQL
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Record
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Record
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FastaM10Parser
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PSSM
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Bio.SearchIO
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Bio.Phylo.BaseTree
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ClustalOmegaCommandline
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Bio.codonalign.codonseq
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ClustalwCommandline
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Bio.Graphics.GenomeDiagram
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DialignCommandline
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MSAProbsCommandline
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Bio.SearchIO.BlastIO.blast_tab
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MafftCommandline
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MutableSeq
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Bio.SearchIO.BlatIO
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MuscleCommandline
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Seq
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Bio.SearchIO.BlastIO.blast_tab
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PrankCommandline
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UnknownSeq
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Bio.Phylo.PAML.chi2
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ProbconsCommandline
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TCoffeeCommandline
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Bio.bgzf
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MultipleSeqAlignment
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SeqRecord
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PairwiseAlignment
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DBSeq
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PairwiseAlignments
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DatabaseLoader
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AlignmentIterator
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BgzfReader
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AlignmentWriter
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RestrictionBatch
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DatabaseLoader
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SequentialAlignmentWriter
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RestrictionType
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DatabaseLoader
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MafIndex
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_SQLiteManySeqFilesDict
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Bio.ExPASy.Enzyme
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(in
DatabaseLoader
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__init__()
(in
AlphabetEncoder
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(in
Bio.ExPASy.Prodoc
)
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(in
DatabaseLoader
)
__init__()
(in
Gapped
)
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(in
Bio.ExPASy.Prosite
)
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(in
DatabaseLoader
)
__init__()
(in
HasStopCodon
)
__read()
(in
Bio.ExPASy.cellosaurus
)
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(in
DatabaseLoader
)
__init__()
(in
AbstractCommandline
)
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(in
Bio.motifs.meme
)
_load_seqfeature_locations()
(in
DatabaseLoader
)
__init__()
(in
ApplicationError
)
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(in
Bio.motifs.meme
)
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(in
DatabaseLoader
)
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(in
_AbstractParameter
)
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(in
Bio.ExPASy.Prodoc
)
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(in
Bio.Phylo.PhyloXMLIO
)
__init__()
(in
_Argument
)
__read_datafile()
(in
Bio.motifs.meme
)
_local_reserved_names
(in
Bio.Application
)
__init__()
(in
_Option
)
__read_hit_alignment()
(in
Bio.Compass
)
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(in
Record
)
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(in
_StaticArgument
)
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(in
Bio.Compass
)
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(in
HiddenMarkovModel
)
__init__()
(in
_Switch
)
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(in
Bio.motifs.mast
)
_logsum()
(in
Bio.MarkovModel
)
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(in
NcbiblastformatterCommandline
)
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(in
Bio.motifs.meme
)
_logvecadd()
(in
Bio.MarkovModel
)
__init__()
(in
NcbiblastnCommandline
)
__read_motif_sequences()
(in
Bio.motifs.meme
)
_LONG_SHORT_MAP
(in
Bio.SearchIO.BlastIO.blast_tab
)
__init__()
(in
NcbiblastpCommandline
)
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(in
Bio.motifs.meme
)
_lower()
(in
Alphabet
)
__init__()
(in
NcbiblastxCommandline
)
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(in
Bio.Compass
)
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(in
AlphabetEncoder
)
__init__()
(in
NcbideltablastCommandline
)
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(in
Bio.Compass
)
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(in
Gapped
)
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(in
NcbimakeblastdbCommandline
)
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(in
Bio.Compass
)
_lower()
(in
HasStopCodon
)
__init__()
(in
NcbipsiblastCommandline
)
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(in
Bio.ExPASy.Prodoc
)
_lower()
(in
ThreeLetterProtein
)
__init__()
(in
NcbirpsblastCommandline
)
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(in
Bio.Compass
)
_lwl85()
(in
Bio.codonalign.codonseq
)
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(in
NcbirpstblastnCommandline
)
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(in
Bio.ExPASy.Prodoc
)
_Mafft
(in
Bio.Align.Applications
)
__init__()
(in
NcbitblastnCommandline
)
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(in
Bio.ExPASy.Prodoc
)
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(in
Bio.Data.IUPACData
)
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(in
NcbitblastxCommandline
)
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(in
Bio.Compass
)
_make_dssp_dict()
(in
Bio.PDB.DSSP'
)
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(in
_NcbibaseblastCommandline
)
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(in
Bio.motifs.mast
)
_make_fragment_list()
(in
Bio.PDB.FragmentMapper'
)
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(in
_Ncbiblast2SeqCommandline
)
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(in
Bio.motifs.meme
)
_make_list()
(in
PrintFormat
)
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(in
_NcbiblastCommandline
)
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(in
Bio.ExPASy.Prodoc
)
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(in
PrintFormat
)
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(in
_NcbiblastMain2SeqCommandline
)
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(in
Bio.Compass
)
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(in
PrintFormat
)
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(in
BlastParser
)
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(in
Bio.motifs.meme
)
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(in
PrintFormat
)
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(in
_XMLparser
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(in
Bio.Compass
)
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(in
PrintFormat
)
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(in
BlastTableEntry
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(in
MultipleSeqAlignment
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(in
PrintFormat
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(in
BlastTableReader
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(in
Array
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(in
PrintFormat
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(in
BlastTableRec
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(in
MafIndex
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(in
PrintFormat
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(in
Alignment
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(in
Alphabet
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(in
Bio.SeqIO.SwissIO
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(in
Blast
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AlphabetEncoder
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Bio.Data.IUPACData
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DatabaseReport
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(in
AbstractCommandline
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Bio.cpairwise2
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(in
Description
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(in
ApplicationError
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(in
Bio.pairwise2
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(in
DescriptionExt
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Crystal
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(in
Bio.SeqIO.SwissIO
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DescriptionExtItem
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Hetero
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Parser
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HSP
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NCBICodonTable
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Bio.SearchIO.ExonerateIO._base
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Header
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DictionaryElement
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BioSQL.BioSeq
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MultipleAlignment
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IntegerElement
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Bio.Nexus.Nexus
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PSIBlast
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ListElement
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Bio.Seq
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Parameters
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NoneElement
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FragmentMapper
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Round
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StringElement
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Bio.PDB.FragmentMapper'
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CAPSMap
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UnicodeElement
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Record
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DifferentialCutsite
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Record
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Bio.Phylo.TreeConstruction
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Record
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Record
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Nexus
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Record
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FSSPSumRec
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Bio.phenotype.phen_micro
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Chain
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PosAlign
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Reference
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Crystal
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fff_rec
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Bio.codonalign
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Hetero
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_IndexedSeqFileDict
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Bio.SeqIO.SffIO
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AmbiguousCodonTable
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_SQLiteManySeqFilesDict
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Bio.SearchIO.BlastIO.blast_tab
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AmbiguousForwardTable
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Feature
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Bio.SearchIO.BlastIO.blast_tab
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CodonTable
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Qualifier
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Bio.codonalign.codonseq
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NCBICodonTable
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Atom
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Bio.MarkovModel
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DiffseqCommandline
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DisorderedAtom
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Blunt
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EInvertedCommandline
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Chain
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Ov3
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ETandemCommandline
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Fragment
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Ov5
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Est2GenomeCommandline
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Model
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Unknown
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FConsenseCommandline
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Select
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Ambiguous
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FDNADistCommandline
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Polypeptide
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Defined
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FDNAParsCommandline
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DisorderedResidue
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NotDefined
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FNeighborCommandline
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Residue
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Bio.Affy.CelFile
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FProtDistCommandline
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Structure
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Bio.SearchIO
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FProtParsCommandline
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Vector
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NoCut
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FSeqBootCommandline
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Interaction
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OneCut
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FTreeDistCommandline
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Network
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TwoCuts
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FuzznucCommandline
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Reaction
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Bio.Align.Applications
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FuzzproCommandline
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Graph
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Bio.Align.Applications
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IepCommandline
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MultiGraph
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Record
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NeedleCommandline
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System
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Record
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NeedleallCommandline
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BranchColor
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Record
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PalindromeCommandline
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TreeElement
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Nexus
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Primer3Commandline
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_BitString
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Bio.Blast.Applications
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PrimerSearchCommandline
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_Matrix
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Bio.Blast.Applications
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SeqmatchallCommandline
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Analysis
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Bio.Blast.Applications
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SeqretCommandline
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FormattedSeq
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Bio.Blast.Applications
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StretcherCommandline
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RestrictionBatch
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Bio.codonalign.codonseq
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TranalignCommandline
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RestrictionType
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Bio.PDB.parse_pdb_header'
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WaterCommandline
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Hit
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Record
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_EmbossCommandLine
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HSP
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NNITreeSearcher
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_EmbossMinimalCommandLine
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HSPFragment
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Bio.AlignIO.PhylipIO
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Primers
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QueryResult
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Bio.SeqRecord
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Record
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MutableSeq
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_XMLparser
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Amplifier
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Seq
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Bio.SCOP
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InputRecord
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UnknownSeq
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_BaseSearchObject
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OutputRecord
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AbstractPosition
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Hit
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CorruptedXMLError
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AfterPosition
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HSP
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DataHandler
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BeforePosition
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QueryResult
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DictionaryElement
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BetweenPosition
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Bio.MarkovModel
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CompoundLocation
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_BaseGenBankConsumer
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NoneElement
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Bio.Sequencing.Applications
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NotXMLError
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FeatureLocation
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Bio.Phylo.PhyloXMLIO
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ValidationError
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OneOfPosition
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Bio.SeqIO.SffIO
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Record
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PositionGap
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Bio.Phylo.BaseTree
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Record
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Reference
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BlastParser
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Reference
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SeqFeature
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Bio.GenBank
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Record
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UnknownPosition
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Bio.GenBank
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ContentHandler
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WithinPosition
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Bio.Entrez
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Parser
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SeqRecord
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Bio.SCOP
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Record
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Bio.TogoWS
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Record
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Record
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Bio.File
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FSSPAlignDict
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STSLine
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Bio.SCOP
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FSSPAlignRec
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SequenceLine
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Bio.Application
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FSSPHeader
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AlignmentColumn
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Bio.Wise.psw
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FSSPSumRec
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ColumnUnit
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Bio.Wise.psw
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FSSPMultAlign
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CodonAlphabet
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Bio.Wise.psw
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PosAlign
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PlateRecord
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Nexus
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fff_rec
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WellRecord
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Record
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UndoHandle
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BioSeqDatabase
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Record
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_IndexedSeqFileDict
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DBServer
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Bio.phenotype.phen_micro
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_SQLiteManySeqFilesDict
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Confidence
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AnnotatedChromosomeSegment
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FeatureParser
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RestrictionType
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ChromosomeSegment
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Iterator
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Confidence
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Bio.SeqIO.SnapGeneIO
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Feature
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Confidence
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Bio.SeqIO.SnapGeneIO
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Qualifier
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MutableSeq
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Bio.GenBank
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Record
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Seq
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SummaryInfo
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Reference
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UnknownSeq
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DistanceCalculator
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RecordParser
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SeqMat
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Bio.Phylo.PAML
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InsdcScanner
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DBSeq
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Bio.SearchIO._legacy.NCBIStandalone
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_BaseGenBankConsumer
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_BitString
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Bio
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_FeatureConsumer
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Confidence
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BlastTableReader
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_RecordConsumer
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RestrictionType
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Tree
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FeatureValueCleaner
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Confidence
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PDBParser
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Record
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Confidence
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Residues
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AnnotatedChromosomeSegment
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RestrictionBatch
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BlastXmlIndexer
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Chromosome
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RestrictionType
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SearchIndexer
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ChromosomeSegment
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_BitString
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_DescriptionConsumer
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Organism
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DBSeqRecord
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_BaseExonerateParser
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TelomereSegment
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DBSeqRecord
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Hmmer3TextParser
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_ChromosomeComponent
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DBSeqRecord
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Bio.Phylo.PAML
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ColorSpiral
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DBSeqRecord
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Parser
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ComparativeScatterPlot
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PairwiseAligner
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Bio.Phylo.PAML
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ChromosomeCounts
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AbstractCommandline
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BlastTabParser
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BarChartDistribution
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Array
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BlastTabParser
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DistributionPage
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Chain
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Bio.Phylo.NewickIO
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LineDistribution
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Crystal
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Bio.SeqIO.SnapGeneIO
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AbstractDrawer
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_IndexedSeqFileDict
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PDBParser
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CircularDrawer
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_InMemoryIndex
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BlastTableReader
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ColorTranslator
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__setitem__()
(in
DisorderedEntityWrapper
)
_parse_dna_packet()
(in
Bio.SeqIO.SnapGeneIO
)
__init__()
(in
CrossLink
)
__setitem__()
(in
Vector
)
_parse_feature_description()
(in
Bio.SeqIO.XdnaIO
)
__init__()
(in
Diagram
)
__setitem__()
(in
Events
)
_parse_features_packet()
(in
Bio.SeqIO.SnapGeneIO
)
__init__()
(in
Feature
)
__setitem__()
(in
DistanceMatrix
)
_parse_fields()
(in
BlastTableReader
)
__init__()
(in
FeatureSet
)
__setitem__()
(in
_Matrix
)
_parse_fields_line()
(in
BlastTabParser
)
__init__()
(in
GraphData
)
__setitem__()
(in
Hit
)
_parse_header()
(in
InterproscanXmlParser
)
__init__()
(in
GraphSet
)
__setitem__()
(in
HSP
)
_parse_hit()
(in
BlastXmlParser
)
__init__()
(in
LinearDrawer
)
__setitem__()
(in
QueryResult
)
_parse_hit()
(in
FastaM10Parser
)
__init__()
(in
Track
)
__setitem__()
(in
MutableSeq
)
_parse_hit()
(in
Hmmer3TextParser
)
__init__()
(in
KGMLCanvas
)
__setitem__()
(in
_RestrictedDict
)
_parse_hit()
(in
InterproscanXmlParser
)
__init__()
(in
AbstractDPAlgorithms
)
__setitem__()
(in
PlateRecord
)
_parse_hit_block()
(in
Hhsuite2TextParser
)
__init__()
(in
LogDPAlgorithms
)
__setitem__()
(in
WellRecord
)
_parse_hit_match_block()
(in
Hhsuite2TextParser
)
__init__()
(in
ScaledDPAlgorithms
)
__skip_unused_lines()
(in
Bio.motifs.meme
)
_parse_hit_or_query_line()
(in
Bio.SearchIO.ExonerateIO._base
)
__init__()
(in
HiddenMarkovModel
)
__str__()
(in
PSSM
)
_parse_hsp()
(in
BlastXmlParser
)
__init__()
(in
MarkovModelBuilder
)
__str__()
(in
MultipleSeqAlignment
)
_parse_hsp()
(in
InterproscanXmlParser
)
__init__()
(in
AbstractTrainer
)
__str__()
(in
PairwiseAlignment
)
_parse_iteration()
(in
BlastTableReader
)
__init__()
(in
BaumWelchTrainer
)
__str__()
(in
Array
)
_parse_list()
(in
Nexus
)
__init__()
(in
KnownStateTrainer
)
__str__()
(in
AbstractCommandline
)
_parse_nexus_block()
(in
Nexus
)
__init__()
(in
TrainingSequence
)
__str__()
(in
ApplicationError
)
_parse_notes_packet()
(in
Bio.SeqIO.SnapGeneIO
)
__init__()
(in
_InMemoryIndex
)
__str__()
(in
_AbstractParameter
)
_parse_pdb_header_list()
(in
Bio.PDB.parse_pdb_header'
)
__init__()
(in
_ShelveIndex
)
__str__()
(in
_Argument
)
_parse_phylogeny()
(in
Parser
)
__init__()
(in
KDTree
)
__str__()
(in
_ArgumentList
)
_parse_preamble()
(in
BlastXmlParser
)
__init__()
(in
Record
)
__str__()
(in
_Option
)
_parse_preamble()
(in
FastaM10Parser
)
__init__()
(in
Record
)
__str__()
(in
_StaticArgument
)
_parse_preamble()
(in
Hhsuite2TextParser
)
__init__()
(in
Record
)
__str__()
(in
_Switch
)
_parse_preamble()
(in
Hmmer3TextParser
)
__init__()
(in
KGMLParser
)
__str__()
(in
Alignment
)
_parse_primers_packet()
(in
Bio.SeqIO.SnapGeneIO
)
__init__()
(in
Component
)
__str__()
(in
Description
)
_parse_qblast_ref_page()
(in
Bio.Blast.NCBIWWW
)
__init__()
(in
Entry
)
__str__()
(in
DescriptionExtItem
)
_parse_qresult()
(in
BlastTabParser
)
__init__()
(in
Graphics
)
__str__()
(in
HSP
)
_parse_qresult()
(in
BlastXmlParser
)
__init__()
(in
Pathway
)
__str__()
(in
Chain
)
_parse_qresult()
(in
BlatPslParser
)
__init__()
(in
Reaction
)
__str__()
(in
Crystal
)
_parse_qresult()
(in
_BaseExonerateParser
)
__init__()
(in
Relation
)
__str__()
(in
Hetero
)
_parse_qresult()
(in
FastaM10Parser
)
__init__()
(in
LogisticRegression
)
__str__()
(in
CodonTable
)
_parse_qresult()
(in
Hhsuite2TextParser
)
__init__()
(in
MarkovModel
)
__str__()
(in
InputRecord
)
_parse_qresult()
(in
Hmmer3DomtabParser
)
__init__()
(in
MaxEntropy
)
__str__()
(in
CorruptedXMLError
)
_parse_qresult()
(in
Hmmer3TabParser
)
__init__()
(in
Peaklist
)
__str__()
(in
NotXMLError
)
_parse_qresult()
(in
Hmmer3TextParser
)
__init__()
(in
XpkEntry
)
__str__()
(in
ValidationError
)
_parse_qresult()
(in
InterproscanXmlParser
)
__init__()
(in
NaiveBayes
)
__str__()
(in
Record
)
_parse_query()
(in
BlastTableReader
)
__init__()
(in
Block
)
__str__()
(in
Record
)
_parse_remark_465()
(in
Bio.PDB.parse_pdb_header'
)
__init__()
(in
CharBuffer
)
__str__()
(in
_IndexedSeqFileDict
)
_parse_result_row()
(in
BlastTabParser
)
__init__()
(in
Commandline
)
__str__()
(in
Feature
)
_parse_row()
(in
BlatPslParser
)
__init__()
(in
Nexus
)
__str__()
(in
Qualifier
)
_parse_row()
(in
Hmmer3DomtabParser
)
__init__()
(in
StepMatrix
)
__str__()
(in
Record
)
_parse_row()
(in
Hmmer3TabParser
)
__init__()
(in
Chain
)
__str__()
(in
Reference
)
_parse_sequence()
(in
Parser
)
__init__()
(in
Node
)
__str__()
(in
Record
)
_parse_tag_data()
(in
Bio.SeqIO.AbiIO
)
__init__()
(in
StandardData
)
__str__()
(in
Diagram
)
_parse_taxonomy()
(in
Parser
)
__init__()
(in
NodeData
)
__str__()
(in
FeatureSet
)
_parse_tree()
(in
Parser
)
__init__()
(in
Tree
)
__str__()
(in
GraphData
)
_parse_version()
(in
BlastTableReader
)
__init__()
(in
AbstractAtomPropertyMap
)
__str__()
(in
GraphSet
)
_parse_xrefs()
(in
InterproscanXmlParser
)
__init__()
(in
AbstractPropertyMap
)
__str__()
(in
Track
)
_parse_yn00
(in
Bio.Phylo.PAML
)
__init__()
(in
AbstractResiduePropertyMap
)
__str__()
(in
Record
)
_parser
(in
_BaseExonerateIndexer
)
__init__()
(in
Atom
)
__str__()
(in
Record
)
_part()
(in
Bio.Phylo.Consensus
)
__init__()
(in
DisorderedAtom
)
__str__()
(in
Record
)
_pathway()
(in
Record
)
__init__()
(in
Chain
)
__str__()
(in
Entry
)
_pathway()
(in
Record
)
__init__()
(in
DSSP
)
__str__()
(in
Pathway
)
_pdbid_re
(in
Bio.SCOP.Residues
)
__init__()
(in
ChainSelector
)
__str__()
(in
Reaction
)
_phred_to_illumina_quality_str
(in
Bio.SeqIO.QualityIO
)
__init__()
(in
DisorderedEntityWrapper
)
__str__()
(in
Relation
)
_phred_to_sanger_quality_str
(in
Bio.SeqIO.QualityIO
)
__init__()
(in
Entity
)
__str__()
(in
MarkovModel
)
_phred_to_solexa_quality_str
(in
Bio.SeqIO.QualityIO
)
__init__()
(in
Fragment
)
__str__()
(in
StandardData
)
_PHYLIP_ID_WIDTH
(in
Bio.AlignIO.PhylipIO
)
__init__()
(in
FragmentMapper
)
__str__()
(in
Tree
)
_Phyml
(in
Bio.Phylo.Applications
)
__init__()
(in
ExposureCN
)
__str__()
(in
Interaction
)
_pid_line()
(in
Record
)
__init__()
(in
HSExposureCA
)
__str__()
(in
Network
)
_pir_alphabets
(in
Bio.SeqIO.PirIO
)
__init__()
(in
HSExposureCB
)
__str__()
(in
Reaction
)
_place_labels()
(in
Bio.Graphics.BasicChromosome
)
__init__()
(in
_AbstractHSExposure
)
__str__()
(in
Graph
)
_plate
(in
Bio.phenotype.phen_micro
)
__init__()
(in
MMCIF2Dict
)
__str__()
(in
MultiGraph
)
_platesPrefix
(in
Bio.phenotype.phen_micro
)
__init__()
(in
FastMMCIFParser
)
__str__()
(in
System
)
_platesPrefixMammalian
(in
Bio.phenotype.phen_micro
)
__init__()
(in
MMCIFParser
)
__str__()
(in
BranchColor
)
_populate_meta_data()
(in
StockholmIterator
)
__init__()
(in
Model
)
__str__()
(in
Clade
)
_position
(in
Bio.phenotype.phen_micro
)
__init__()
(in
NACCESS
)
__str__()
(in
Tree
)
_possibly_complemented_complex_location
(in
Bio.GenBank
)
__init__()
(in
NACCESS_atomic
)
__str__()
(in
Accession
)
_POSTGRES_RULES_PRESENT
(in
BioSQL.BioSeqDatabase
)
__init__()
(in
NeighborSearch
)
__str__()
(in
Date
)
_PostgreSQL_dbutils
(in
BioSQL.DBUtils
)
__init__()
(in
PDBIO
)
__str__()
(in
Id
)
_postorder_traverse()
(in
Bio.Phylo.BaseTree
)
__init__()
(in
PDBList
)
__str__()
(in
MolSeq
)
_powers_of_36
(in
Bio.SeqIO.SffIO
)
__init__()
(in
PDBParser
)
__str__()
(in
Phyloxml
)
_PPBuilder
(in
Bio.PDB.Polypeptide
)
__init__()
(in
PSEA
)
__str__()
(in
Polygon
)
_Prank
(in
Bio.Align.Applications
)
__init__()
(in
CaPPBuilder
)
__str__()
(in
Taxonomy
)
_PRECISION
(in
Bio.pairwise2
)
__init__()
(in
PPBuilder
)
__str__()
(in
Uri
)
_preorder_traverse()
(in
Bio.Phylo.BaseTree
)
__init__()
(in
_PPBuilder
)
__str__()
(in
_Matrix
)
_prep_coord()
(in
HSPFragment
)
__init__()
(in
QCPSuperimposer
)
__str__()
(in
FileRecord
)
_prep_fields()
(in
BlastTabParser
)
__init__()
(in
DisorderedResidue
)
__str__()
(in
Record
)
_prep_frame()
(in
HSPFragment
)
__init__()
(in
Residue
)
__str__()
(in
RestrictionBatch
)
_prep_strand()
(in
HSPFragment
)
__init__()
(in
ResidueDepth
)
__str__()
(in
RestrictionType
)
_prim()
(in
Bio.codonalign.codonalignment
)
__init__()
(in
Structure
)
__str__()
(in
Record
)
_print_default_format_warning()
(in
PDBList
)
__init__()
(in
StructureAlignment
)
__str__()
(in
Record
)
_print_name()
(in
TaggingConsumer
)
__init__()
(in
StructureBuilder
)
__str__()
(in
Record
)
_Probcons
(in
Bio.Align.Applications
)
__init__()
(in
Superimposer
)
__str__()
(in
Domain
)
_process()
(in
Record
)
__init__()
(in
MMCIFIO
)
__str__()
(in
Record
)
_process()
(in
Record
)
__init__()
(in
StructureDecoder
)
__str__()
(in
Node
)
_process()
(in
Record
)
__init__()
(in
MMTFIO
)
__str__()
(in
Residues
)
_process()
(in
Record
)
__init__()
(in
Vector
)
__str__()
(in
Hit
)
_process()
(in
SeqMap
)
__init__()
(in
Network
)
__str__()
(in
HSP
)
_process_score_line()
(in
Hhsuite2TextParser
)
__init__()
(in
Reaction
)
__str__()
(in
HSPFragment
)
_product()
(in
Record
)
__init__()
(in
Graph
)
__str__()
(in
QueryResult
)
_PROGRAM
(in
Bio.SearchIO.HHsuiteIO.hhsuite2_text
)
__init__()
(in
MultiGraph
)
__str__()
(in
MutableSeq
)
_project_line()
(in
Record
)
__init__()
(in
System
)
__str__()
(in
Seq
)
_PSIBlastConsumer
(in
Bio.SearchIO._legacy.NCBIStandalone
)
__init__()
(in
FastTreeCommandline
)
__str__()
(in
UnknownSeq
)
_PTR_ID_DESC_SEQLEN
(in
Bio.SearchIO.FastaIO
)
__init__()
(in
PhymlCommandline
)
__str__()
(in
AfterPosition
)
_PTR_ROW_CHECK
(in
Bio.SearchIO.BlatIO
)
__init__()
(in
RaxmlCommandline
)
__str__()
(in
BeforePosition
)
_pubmed_line()
(in
Reference
)
__init__()
(in
BranchColor
)
__str__()
(in
BetweenPosition
)
_pwm
(in
Bio.motifs
)
__init__()
(in
Clade
)
__str__()
(in
CompoundLocation
)
_py3k
(in
Bio
)
__init__()
(in
Tree
)
__str__()
(in
ExactPosition
)
_python_make_score_matrix_fast()
(in
Bio.pairwise2
)
__init__()
(in
Clade
)
__str__()
(in
FeatureLocation
)
_python_rint()
(in
Bio.pairwise2
)
__init__()
(in
Tree
)
__str__()
(in
OneOfPosition
)
_q()
(in
Bio.KEGG.REST
)
__init__()
(in
Parser
)
__str__()
(in
PositionGap
)
_q()
(in
Bio.codonalign.codonseq
)
__init__()
(in
Writer
)
__str__()
(in
Reference
)
_QRE_ID_LEN
(in
Bio.SearchIO.HmmerIO.hmmer3_text
)
__init__()
(in
Clade
)
__str__()
(in
SeqFeature
)
_QRE_ID_LEN_PTN
(in
Bio.SearchIO.HmmerIO.hmmer3_text
)
__init__()
(in
Tree
)
__str__()
(in
WithinPosition
)
_qresult_index()
(in
BlastTabIndexer
)
__init__()
(in
Parser
)
__str__()
(in
SeqRecord
)
_qresult_index_commented()
(in
BlastTabIndexer
)
__init__()
(in
Writer
)
__str__()
(in
SeqMat
)
_query_end_get()
(in
HSP
)
__init__()
(in
Clade
)
__str__()
(in
Statistics
)
_query_end_get()
(in
HSPFragment
)
__init__()
(in
Tree
)
__str__()
(in
CodonAlignment
)
_query_end_set()
(in
HSPFragment
)
__init__()
(in
Parser
)
__str__()
(in
Instances
)
_query_frame_get()
(in
HSPFragment
)
__init__()
(in
Writer
)
__str__()
(in
Motif
)
_query_frame_set()
(in
HSPFragment
)
__init__()
(in
Paml
)
__str__()
(in
Record
)
_query_get()
(in
HSPFragment
)
__init__()
(in
Baseml
)
__str__()
(in
Motif
)
_query_id_idx
(in
Hmmer3DomtabHmmhitIndexer
)
__init__()
(in
Codeml
)
__str__()
(in
Record
)
_query_id_idx
(in
Hmmer3DomtabHmmqueryIndexer
)
__init__()
(in
Yn00
)
__str__()
(in
JASPAR5
)
_query_id_idx
(in
Hmmer3TabIndexer
)
__init__()
(in
Accession
)
__str__()
(in
GenericPositionMatrix
)
_query_inter_ranges_get()
(in
HSP
)
__init__()
(in
Annotation
)
__str__()
(in
Record
)
_query_inter_spans_get()
(in
HSP
)
__init__()
(in
BinaryCharacters
)
__str__()
(in
Record
)
_query_mark
(in
_BaseExonerateIndexer
)
__init__()
(in
BranchColor
)
__str__()
(in
Record
)
_query_mark
(in
ExonerateCigarIndexer
)
__init__()
(in
Clade
)
__str__()
(in
PlateRecord
)
_query_mark
(in
ExonerateTextIndexer
)
__init__()
(in
CladeRelation
)
__str__()
(in
WellRecord
)
_query_mark
(in
ExonerateVulgarIndexer
)
__init__()
(in
Confidence
)
__str__()
(in
DBSeq
)
_query_range_get()
(in
HSP
)
__init__()
(in
Date
)
__sub__()
(in
Atom
)
_query_range_get()
(in
HSPFragment
)
__init__()
(in
Distribution
)
__sub__()
(in
DisorderedEntityWrapper
)
_query_re
(in
_HSPConsumer
)
__init__()
(in
DomainArchitecture
)
__sub__()
(in
Fragment
)
_query_set()
(in
HSPFragment
)
__init__()
(in
Events
)
__sub__()
(in
Vector
)
_query_span_get()
(in
HSP
)
__init__()
(in
Id
)
__sub__()
(in
Confidence
)
_query_span_get()
(in
HSPFragment
)
__init__()
(in
MolSeq
)
__sub__()
(in
SeqMat
)
_query_start_get()
(in
HSP
)
__init__()
(in
Other
)
__sub__()
(in
PlateRecord
)
_query_start_get()
(in
HSPFragment
)
__init__()
(in
Phylogeny
)
__sub__()
(in
WellRecord
)
_query_start_set()
(in
HSPFragment
)
__init__()
(in
Phyloxml
)
__truediv__()
(in
Vector
)
_query_strand_get()
(in
HSPFragment
)
__init__()
(in
Point
)
__truediv__()
(in
Confidence
)
_query_strand_set()
(in
HSPFragment
)
__init__()
(in
Polygon
)
__truediv__()
(in
RestrictionBatch
)
_random_norm()
(in
Bio.MarkovModel
)
__init__()
(in
Property
)
__truediv__()
(in
RestrictionType
)
_Raxml
(in
Bio.Phylo.Applications
)
__init__()
(in
ProteinDomain
)
__version
(in
_InMemoryIndex
)
_re_alb_line2coords
(in
Bio.Wise.dnal
)
__init__()
(in
Reference
)
__version
(in
_ShelveIndex
)
_RE_ALN_ROW
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__init__()
(in
Sequence
)
__version_key
(in
_InMemoryIndex
)
_RE_ATTR
(in
Bio.SearchIO.FastaIO
)
__init__()
(in
SequenceRelation
)
__version_key
(in
_ShelveIndex
)
_RE_CIGAR
(in
Bio.SearchIO.ExonerateIO.exonerate_cigar
)
__init__()
(in
Taxonomy
)
__warningregistry__
(in
Bio.Align.substitution_matrices
)
_re_complex_compound
(in
Bio.GenBank
)
__init__()
(in
Uri
)
__warningregistry__
(in
Bio.Alphabet
)
_re_complex_location
(in
Bio.GenBank
)
__init__()
(in
Parser
)
__warningregistry__
(in
Bio.Index
)
_RE_END_EXC
(in
Bio.SearchIO.FastaIO
)
__init__()
(in
Writer
)
__warningregistry__
(in
Bio.KDTree
)
_RE_EXON
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__init__()
(in
DistanceCalculator
)
__warningregistry__
(in
Bio.Statistics
)
_RE_EXON_LEN
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__init__()
(in
DistanceMatrix
)
__warningregistry__
(in
Bio.codonalign
)
_RE_FLAVS
(in
Bio.SearchIO.FastaIO
)
__init__()
(in
DistanceTreeConstructor
)
__warningregistry__
(in
Bio.phenotype
)
_RE_GAPOPEN
(in
Bio.SearchIO.BlastIO.blast_tab
)
__init__()
(in
NNITreeSearcher
)
__warningregistry__
(in
Bio.triefind
)
_RE_HIT_BLOCK_DESC
(in
Bio.SearchIO.HHsuiteIO.hhsuite2_text
)
__init__()
(in
ParsimonyScorer
)
__xor__()
(in
_BitString
)
_RE_HIT_BLOCK_START
(in
Bio.SearchIO.HHsuiteIO.hhsuite2_text
)
__init__()
(in
ParsimonyTreeConstructor
)
_abi_parse_header()
(in
Bio.SeqIO.AbiIO
)
_RE_ID_DESC_PAIRS_PATTERN
(in
Bio.SearchIO.BlastIO.blast_xml
)
__init__()
(in
_Matrix
)
_abi_trim()
(in
Bio.SeqIO.AbiIO
)
_RE_ID_DESC_PATTERN
(in
Bio.SearchIO.BlastIO.blast_xml
)
__init__()
(in
GenePopController
)
_AbiTrimIterator()
(in
Bio.SeqIO.AbiIO
)
_RE_ID_DESC_SEQLEN
(in
Bio.SearchIO.FastaIO
)
__init__()
(in
_FileIterator
)
_AbstractDrawer
(in
Bio.Graphics.GenomeDiagram
)
_RE_ID_DESC_SEQLEN_IDX
(in
Bio.SearchIO.FastaIO
)
__init__()
(in
_GenePopCommandline
)
_AbstractHSExposure
(in
Bio.PDB.HSExposure
)
_RE_MATCH_BLOCK_HIT_SEQ
(in
Bio.SearchIO.HHsuiteIO.hhsuite2_text
)
__init__()
(in
EasyController
)
_AbstractParameter
(in
Bio.Application
)
_RE_MATCH_BLOCK_QUERY_SEQ
(in
Bio.SearchIO.HHsuiteIO.hhsuite2_text
)
__init__()
(in
FileRecord
)
_accept()
(in
_PPBuilder
)
_RE_NER
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__init__()
(in
Record
)
_accession_line()
(in
Record
)
_RE_NER_LEN
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__init__()
(in
Record
)
_add()
(in
ScoreDistribution
)
_re_oneof_position
(in
Bio.GenBank
)
__init__()
(in
PrintFormat
)
_add_bioentry_dbxref()
(in
DatabaseLoader
)
_RE_OPT
(in
Bio.SearchIO.HmmerIO.hmmer3_text
)
__init__()
(in
Analysis
)
_add_dbxref()
(in
DatabaseLoader
)
_RE_PROGRAM
(in
Bio.SearchIO.HmmerIO.hmmer3_text
)
__init__()
(in
FormattedSeq
)
_add_feature()
(in
_RecordConsumer
)
_re_prop_name
(in
Bio.Application
)
__init__()
(in
RestrictionBatch
)
_add_nodedata()
(in
Tree
)
_RE_QUERY
(in
Bio.SearchIO.HHsuiteIO.hhsuite2_text
)
__init__()
(in
RestrictionType
)
_add_numbering_table()
(in
FSSPAlign
)
_RE_ROW_CHECK
(in
Bio.SearchIO.BlatIO
)
__init__()
(in
Astral
)
_add_seqfeature_dbxref()
(in
DatabaseLoader
)
_RE_ROW_CHECK_IDX
(in
Bio.SearchIO.BlatIO
)
__init__()
(in
Index
)
_add_subtree()
(in
Tree
)
_RE_SCODON_END
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__init__()
(in
Record
)
_AddTellHandle
(in
Bio.SeqIO.SffIO
)
_RE_SCODON_START
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__init__()
(in
Record
)
_adjust_aa_seq()
(in
Bio.SearchIO.ExonerateIO._base
)
_re_search()
(in
Bio.SearchIO._legacy.NCBIStandalone
)
__init__()
(in
Record
)
_adjust_charlabels()
(in
Nexus
)
_RE_SHIFTS
(in
Bio.SearchIO.ExonerateIO._base
)
__init__()
(in
Domain
)
_adjust_coords()
(in
BlastTabWriter
)
_re_simple_compound
(in
Bio.GenBank
)
__init__()
(in
Record
)
_adjust_lines()
(in
Bio.Nexus.Nexus
)
_re_simple_location
(in
Bio.GenBank
)
__init__()
(in
Node
)
_adjust_output()
(in
BlastTabWriter
)
_RE_START_EXC
(in
Bio.SearchIO.FastaIO
)
__init__()
(in
Res
)
_adjust_output()
(in
BlastXmlWriter
)
_RE_TRANS
(in
Bio.SearchIO.ExonerateIO._base
)
__init__()
(in
SeqMap
)
_alb_line2coords()
(in
Bio.Wise.dnal
)
_re_unit
(in
Bio.Wise.psw
)
__init__()
(in
SeqMapIndex
)
_align()
(in
QCPSuperimposer
)
_RE_VCOMP
(in
Bio.SearchIO.ExonerateIO.exonerate_vulgar
)
__init__()
(in
Residues
)
_align()
(in
Bio.pairwise2
)
_RE_VERSION
(in
Bio.SearchIO.BlastIO.blast_xml
)
__init__()
(in
Scop
)
_align_shift_recs()
(in
Bio.codonalign
)
_RE_VERSION
(in
Bio.SearchIO.HmmerIO.hmmer3_text
)
__init__()
(in
SVDSuperimposer
)
_aligners
(in
Bio.Align
)
_RE_VULGAR
(in
Bio.SearchIO.ExonerateIO.exonerate_vulgar
)
__init__()
(in
BlastTabIndexer
)
_AlignmentConsumer
(in
Bio.SearchIO._legacy.NCBIStandalone
)
_re_within_position
(in
Bio.GenBank
)
__init__()
(in
BlastTabParser
)
_all_blank()
(in
MarkovModelBuilder
)
_reaction()
(in
Record
)
__init__()
(in
BlastTabWriter
)
_all_pseudo()
(in
MarkovModelBuilder
)
_read()
(in
Bio.SeqIO.GckIO
)
__init__()
(in
BlastTextParser
)
_allowed_lookups
(in
BioSQL.BioSeqDatabase
)
_read()
(in
Bio.SeqIO.XdnaIO
)
__init__()
(in
BlastXmlIndexer
)
_aln_get()
(in
HSPFragment
)
_read()
(in
Bio.SwissProt
)
__init__()
(in
BlastXmlParser
)
_ALN_MARK
(in
_BaseExonerateParser
)
_read()
(in
Bio.UniGene
)
__init__()
(in
BlastXmlWriter
)
_ALN_MARK
(in
ExonerateCigarParser
)
_read_alignment()
(in
ExonerateTextParser
)
__init__()
(in
_BlastXmlGenerator
)
_ALN_MARK
(in
ExonerateTextParser
)
_read_allele_freq_table()
(in
Bio.PopGen.GenePop.Controller
)
__init__()
(in
BlatPslIndexer
)
_ALN_MARK
(in
ExonerateVulgarParser
)
_read_alphabet()
(in
Bio.motifs.minimal
)
__init__()
(in
BlatPslParser
)
_aln_span_get()
(in
HSP
)
_read_background()
(in
Bio.motifs.minimal
)
__init__()
(in
BlatPslWriter
)
_aln_span_get()
(in
HSPFragment
)
_read_cc()
(in
Bio.SwissProt
)
__init__()
(in
_BaseExonerateParser
)
_aln_span_set()
(in
HSPFragment
)
_read_dicts()
(in
Bio.NMR.xpktools
)
__init__()
(in
FastaM10Indexer
)
_alphabet_from_input()
(in
FreqTable
)
_read_dr()
(in
Bio.SwissProt
)
__init__()
(in
FastaM10Parser
)
_alphabet_from_matrix()
(in
SeqMat
)
_read_dt()
(in
Bio.SwissProt
)
__init__()
(in
Hhsuite2TextParser
)
_alphabet_get()
(in
HSPFragment
)
_read_feature()
(in
Bio.SeqIO.XdnaIO
)
__init__()
(in
_BaseHmmerTextIndexer
)
_alphabet_set()
(in
HSPFragment
)
_read_fragments()
(in
Bio.PDB.FragmentMapper'
)
__init__()
(in
Hmmer2TextParser
)
_append()
(in
MultipleSeqAlignment
)
_read_ft()
(in
Bio.SwissProt
)
__init__()
(in
Hmmer3DomtabHmmhitWriter
)
_apply_block_structure()
(in
Nexus
)
_read_headed_triangle_matrix()
(in
Bio.PopGen.GenePop.Controller
)
__init__()
(in
Hmmer3TabParser
)
_argmaxes()
(in
Bio.MarkovModel
)
_read_header()
(in
Bio._utils
)
__init__()
(in
Hmmer3TabWriter
)
_Argument
(in
Bio.Application
)
_read_id()
(in
Bio.SwissProt
)
__init__()
(in
Hmmer3TextParser
)
_ArgumentList
(in
Bio.Application
)
_read_jaspar()
(in
Bio.motifs.jaspar
)
__init__()
(in
InterproscanXmlParser
)
_as_bytes()
(in
Bio._py3k
)
_read_key_value()
(in
Bio.Geo
)
__init__()
(in
SearchIndexer
)
_as_unicode()
(in
Bio._py3k
)
_read_kw()
(in
Bio.SwissProt
)
__init__()
(in
BlastErrorParser
)
_assign_atom_mass()
(in
Atom
)
_read_lpm()
(in
Bio.motifs.minimal
)
__init__()
(in
BlastParser
)
_assign_element()
(in
Atom
)
_read_motif_name()
(in
Bio.motifs.minimal
)
__init__()
(in
Iterator
)
_ATOM_FORMAT_STRING
(in
Bio.PDB.PDBIO'
)
_read_motif_statistics()
(in
Bio.motifs.minimal
)
__init__()
(in
PSIBlastParser
)
_atom_name_dict
(in
Bio.PDB.Residue
)
_read_oh()
(in
Bio.SwissProt
)
__init__()
(in
_BlastConsumer
)
_atomic_radii
(in
Bio.PDB.ResidueDepth'
)
_read_overhang()
(in
Bio.SeqIO.XdnaIO
)
__init__()
(in
_BlastErrorConsumer
)
_attr_DBRef()
(in
SeqXmlIterator
)
_read_ox()
(in
Bio.SwissProt
)
__init__()
(in
_PSIBlastConsumer
)
_attr_entry()
(in
SeqXmlIterator
)
_read_p4string()
(in
Bio.SeqIO.GckIO
)
__init__()
(in
_Scanner
)
_attr_property()
(in
SeqXmlIterator
)
_read_packet()
(in
Bio.SeqIO.GckIO
)
__init__()
(in
TaggingConsumer
)
_attr_seqXML()
(in
SeqXmlIterator
)
_read_pe()
(in
Bio.SwissProt
)
__init__()
(in
Hit
)
_attr_species()
(in
SeqXmlIterator
)
_read_pfm()
(in
Bio.motifs.jaspar
)
__init__()
(in
HSP
)
_attribute_matcher()
(in
Bio.Phylo.BaseTree
)
_read_pfm_four_columns()
(in
Bio.motifs.pfm
)
__init__()
(in
HSPFragment
)
_attributes()
(in
XMLRecordIterator
)
_read_pfm_four_rows()
(in
Bio.motifs.pfm
)
__init__()
(in
QueryResult
)
_augment_blast_hsp()
(in
Bio.SearchIO.BlastIO.blast_tab
)
_read_pstring()
(in
Bio.SeqIO.GckIO
)
__init__()
(in
MutableSeq
)
_authors_line()
(in
Reference
)
_read_pstring()
(in
Bio.SeqIO.XdnaIO
)
__init__()
(in
Seq
)
_backward()
(in
Bio.MarkovModel
)
_read_pstring_as_integer()
(in
Bio.SeqIO.XdnaIO
)
__init__()
(in
UnknownSeq
)
_backward_recursion()
(in
AbstractDPAlgorithms
)
_read_rc()
(in
Bio.SwissProt
)
__init__()
(in
CompoundLocation
)
_backward_recursion()
(in
ScaledDPAlgorithms
)
_read_rn()
(in
Bio.SwissProt
)
__init__()
(in
FeatureLocation
)
_base
(in
Bio.SearchIO.ExonerateIO
)
_read_rx()
(in
Bio.SwissProt
)
__init__()
(in
PositionGap
)
_base
(in
Bio.SearchIO.HmmerIO
)
_read_sites()
(in
Bio.motifs.jaspar
)
__init__()
(in
Reference
)
_base
(in
Bio.SearchIO._model
)
_read_table()
(in
Bio.PopGen.GenePop.Controller
)
__init__()
(in
SeqFeature
)
_base_count_line()
(in
Record
)
_read_triangle_matrix()
(in
Bio.PopGen.GenePop.Controller
)
__init__()
(in
FastaTwoLineWriter
)
_BASE_URL
(in
Bio.TogoWS
)
_read_until()
(in
Hhsuite2TextParser
)
__init__()
(in
FastaWriter
)
_BaseExonerateIndexer
(in
Bio.SearchIO.ExonerateIO._base
)
_read_until()
(in
Hmmer3TextParser
)
__init__()
(in
SequenceIterator
)
_BaseExonerateParser
(in
Bio.SearchIO.ExonerateIO._base
)
_read_version()
(in
Bio.motifs.minimal
)
__init__()
(in
SequenceWriter
)
_BaseGenBankConsumer
_read_vertex_array()
(in
Bio.PDB.ResidueDepth'
)
__init__()
(in
SequentialSequenceWriter
)
_BaseHmmerTextIndexer
(in
Bio.SearchIO.HmmerIO._base
)
_readline_and_check_start()
(in
Bio.MarkovModel
)
__init__()
(in
NibWriter
)
_BaseHSP
(in
Bio.SearchIO._model._base
)
_RecordConsumer
__init__()
(in
PhdWriter
)
_BaseSearchObject
(in
Bio.SearchIO._model._base
)
_recover_alignments()
(in
Bio.pairwise2
)
__init__()
(in
PirWriter
)
_baum_welch()
(in
Bio.MarkovModel
)
_reference_line()
(in
Reference
)
__init__()
(in
QualPhredWriter
)
_baum_welch_one()
(in
Bio.MarkovModel
)
_region2bin()
(in
MafIndex
)
__init__()
(in
SeqXmlIterator
)
_between_location
(in
Bio.GenBank
)
_remark_line()
(in
Reference
)
__init__()
(in
SeqXmlWriter
)
_bgzf_eof
(in
Bio.bgzf
)
_remove_newlines()
(in
_BaseGenBankConsumer
)
__init__()
(in
XMLRecordIterator
)
_bgzf_header
(in
Bio.bgzf
)
_remove_spaces()
(in
_BaseGenBankConsumer
)
__init__()
(in
SffWriter
)
_bgzf_magic
(in
Bio.bgzf
)
_reorient_starts()
(in
Bio.SearchIO.BlatIO
)
__init__()
(in
_AddTellHandle
)
_binary_to_string_handle()
(in
Bio._py3k
)
_replace_parenthesized_ambigs()
(in
Bio.Nexus.Nexus
)
__init__()
(in
_PacketIterator
)
_BinaryFormats
(in
Bio.SeqIO
)
_replace_wspace()
(in
Bio.Phylo.PhyloXMLIO
)
__init__()
(in
Parser
)
_BitString
(in
Bio.Phylo.Consensus
)
_requires_newline()
(in
MMCIFIO
)
__init__()
(in
IntelliGeneticsRandomAccess
)
_bitstring_topology()
(in
Bio.Phylo.Consensus
)
_requires_quote()
(in
MMCIFIO
)
__init__()
(in
SeqFileRandomAccess
)
_BlastConsumer
(in
Bio.SearchIO._legacy.NCBIStandalone
)
_reserved_names
(in
Bio.Application
)
__init__()
(in
SequentialSeqFileRandomAccess
)
_BlastErrorConsumer
(in
Bio.SearchIO._legacy.NCBIStandalone
)
_reset_full_id()
(in
Entity
)
__init__()
(in
SffRandomAccess
)
_BlastXmlGenerator
(in
Bio.SearchIO.BlastIO.blast_xml
)
_resolve()
(in
Nexus
)
__init__()
(in
SeqRecord
)
_boundaries()
(in
Analysis
)
_RestrictedDict
(in
Bio.SeqRecord
)
__init__()
(in
_RestrictedDict
)
_build_align_cmdline()
(in
Bio.Wise
)
_restrictionbatch
(in
Bio.Restriction.Restriction
)
__init__()
(in
CodonAdaptationIndex
)
_build_comments()
(in
BlastTabWriter
)
_retrieve_annotations()
(in
BioSQL.BioSeq
)
__init__()
(in
IsoelectricPoint
)
_build_dnal_cmdline()
(in
Bio.Wise.dnal
)
_retrieve_comment()
(in
BioSQL.BioSeq
)
__init__()
(in
ProteinAnalysis
)
_build_exp_freq_mat()
(in
Bio.SubsMat
)
_retrieve_dbxrefs()
(in
BioSQL.BioSeq
)
__init__()
(in
ACEFileRecord
)
_build_header()
(in
BlatPslWriter
)
_retrieve_features()
(in
BioSQL.BioSeq
)
__init__()
(in
Contig
)
_build_header()
(in
Hmmer3DomtabHmmhitWriter
)
_retrieve_location_qualifier_value()
(in
BioSQL.BioSeq
)
__init__()
(in
Reads
)
_build_header()
(in
Hmmer3TabWriter
)
_retrieve_qualifier_value()
(in
BioSQL.BioSeq
)
__init__()
(in
af
)
_build_index()
(in
_SQLiteManySeqFilesDict
)
_retrieve_reference()
(in
BioSQL.BioSeq
)
__init__()
(in
bs
)
_build_log_odds_mat()
(in
Bio.SubsMat
)
_retrieve_seq()
(in
BioSQL.BioSeq
)
__init__()
(in
ct
)
_build_obs_freq_mat()
(in
Bio.SubsMat
)
_retrieve_seq_len()
(in
BioSQL.BioSeq
)
__init__()
(in
ds
)
_build_protein_matrix()
(in
DistanceCalculator
)
_retrieve_taxon()
(in
BioSQL.BioSeq
)
__init__()
(in
qa
)
_build_row()
(in
BlatPslWriter
)
_rev_modify()
(in
NoCut
)
__init__()
(in
rd
)
_build_row()
(in
Hmmer3DomtabHmmhitWriter
)
_rev_modify()
(in
OneCut
)
__init__()
(in
rt
)
_build_row()
(in
Hmmer3TabWriter
)
_rev_modify()
(in
TwoCuts
)
__init__()
(in
wa
)
_build_rows()
(in
BlastTabWriter
)
_reverse_matrices()
(in
Bio.pairwise2
)
__init__()
(in
wr
)
_build_structure()
(in
FastMMCIFParser
)
_rms()
(in
QCPSuperimposer
)
__init__()
(in
NovoalignCommandline
)
_build_structure()
(in
MMCIFParser
)
_rms()
(in
SVDSuperimposer
)
__init__()
(in
BwaAlignCommandline
)
_build_subs_mat()
(in
Bio.SubsMat
)
_rna_complement_table
(in
Bio.Seq
)
__init__()
(in
BwaBwaswCommandline
)
_bwa
(in
Bio.Sequencing.Applications
)
_run_genepop()
(in
GenePopController
)
__init__()
(in
BwaIndexCommandline
)
_BYTEFMT
(in
Bio.SeqIO.AbiIO
)
_safe_float()
(in
Bio.SearchIO._legacy.NCBIStandalone
)
__init__()
(in
BwaMemCommandline
)
_bytes_BC
(in
Bio.bgzf
)
_safe_int()
(in
Bio.SearchIO._legacy.NCBIStandalone
)
__init__()
(in
BwaSampeCommandline
)
_bytes_bytearray_to_str()
(in
Bio._py3k
)
_sample
(in
Bio.phenotype.phen_micro
)
__init__()
(in
BwaSamseCommandline
)
_bytes_to_string()
(in
Bio._py3k
)
_samtools
(in
Bio.Sequencing.Applications
)
__init__()
(in
SamtoolsCalmdCommandline
)
_calc_diversities_fis()
(in
GenePopController
)
_save_dict()
(in
MMCIFIO
)
__init__()
(in
SamtoolsCatCommandline
)
_calc_empirical_expects()
(in
Bio.MaxEntropy
)
_save_structure()
(in
MMCIFIO
)
__init__()
(in
SamtoolsFaidxCommandline
)
_calc_f_sharp()
(in
Bio.MaxEntropy
)
_save_structure()
(in
MMTFIO
)
__init__()
(in
SamtoolsFixmateCommandline
)
_calc_ibd()
(in
GenePopController
)
_savedata()
(in
Record
)
__init__()
(in
SamtoolsIdxstatsCommandline
)
_calc_millibad()
(in
Bio.SearchIO.BlatIO
)
_savekmeans()
(in
Record
)
__init__()
(in
SamtoolsIndexCommandline
)
_calc_model_expects()
(in
Bio.MaxEntropy
)
_savetree()
(in
Record
)
__init__()
(in
SamtoolsMergeCommandline
)
_calc_p_class_given_x()
(in
Bio.MaxEntropy
)
_sbjct_re
(in
_HSPConsumer
)
__init__()
(in
SamtoolsMpileupCommandline
)
_calc_score()
(in
Bio.SearchIO.BlatIO
)
_scan_alignment_header()
(in
_Scanner
)
__init__()
(in
SamtoolsPhaseCommandline
)
_calculate()
(in
Bio.motifs.matrix
)
_scan_alignments()
(in
_Scanner
)
__init__()
(in
SamtoolsReheaderCommandline
)
_calculate_emissions()
(in
Bio.HMM.MarkovModel
)
_scan_database_report()
(in
_Scanner
)
__init__()
(in
SamtoolsRmdupCommandline
)
_calculate_from_transitions()
(in
Bio.HMM.MarkovModel
)
_scan_descriptions()
(in
_Scanner
)
__init__()
(in
SamtoolsTargetcutCommandline
)
_calculate_s_value()
(in
ScaledDPAlgorithms
)
_scan_header()
(in
_Scanner
)
__init__()
(in
SamtoolsVersion0xSortCommandline
)
_calculate_to_transitions()
(in
Bio.HMM.MarkovModel
)
_scan_hsp()
(in
_Scanner
)
__init__()
(in
SamtoolsVersion1xSortCommandline
)
_case_less()
(in
Alphabet
)
_scan_hsp_alignment()
(in
_Scanner
)
__init__()
(in
SamtoolsViewCommandline
)
_cdao_owl
(in
Bio.Phylo
)
_scan_hsp_header()
(in
_Scanner
)
__init__()
(in
Record
)
_chain_id_iterator()
(in
MMTFIO
)
_scan_masterslave_alignment()
(in
_Scanner
)
__init__()
(in
FreqTable
)
_changeset()
(in
Nexus
)
_scan_one_pairwise_alignment()
(in
_Scanner
)
__init__()
(in
SeqMat
)
_chargeR()
(in
IsoelectricPoint
)
_scan_pairwise_alignments()
(in
_Scanner
)
__init__()
(in
Record
)
_charlabels()
(in
Nexus
)
_scan_parameters()
(in
_Scanner
)
__init__()
(in
Record
)
_charpartition()
(in
Nexus
)
_scan_rounds()
(in
_Scanner
)
__init__()
(in
Reference
)
_charset()
(in
Nexus
)
_Scanner
(in
Bio.SearchIO._legacy.NCBIStandalone
)
__init__()
(in
ProtsimLine
)
_charstatelabels()
(in
Nexus
)
_score_e_re
(in
Bio.SearchIO._legacy.NCBIStandalone
)
__init__()
(in
Record
)
_check()
(in
Bio.SeqUtils.MeltingTemp
)
_SCORE_GAP_EXTENSION
(in
Bio.Wise.dnal
)
__init__()
(in
STSLine
)
_check_bases()
(in
Bio.Restriction.Restriction
)
_SCORE_GAP_START
(in
Bio.Wise.dnal
)
__init__()
(in
SequenceLine
)
_check_corr()
(in
Bio.codonalign
)
_SCORE_MATCH
(in
Bio.Wise.dnal
)
__init__()
(in
Statistics
)
_check_eof()
(in
Bio.SeqIO.SffIO
)
_SCORE_MISMATCH
(in
Bio.Wise.dnal
)
__init__()
(in
AlignmentColumn
)
_check_mode()
(in
Bio.SeqIO.SffIO
)
_search()
(in
NonPalindromic
)
__init__()
(in
ColumnUnit
)
_check_str()
(in
Bio.Phylo.PhyloXML
)
_search()
(in
Palindromic
)
__init__()
(in
BgzfReader
)
_check_taxlabels()
(in
Nexus
)
_search_db_names
(in
Bio.TogoWS
)
__init__()
(in
BgzfWriter
)
_check_type_compatible()
(in
Bio.Alphabet
)
_segment_line()
(in
Record
)
__init__()
(in
CodonAlignment
)
_check_value()
(in
AbstractCommandline
)
_select
(in
Bio.PDB.PDBIO'
)
__init__()
(in
CodonSeq
)
_chop_end_codes()
(in
Bio.PDB.parse_pdb_header'
)
_select
(in
Bio.PDB.mmcifio
)
__init__()
(in
kNN
)
_chop_end_misc()
(in
Bio.PDB.parse_pdb_header'
)
_select
(in
Bio.PDB.mmtf.mmtfio
)
__init__()
(in
Instances
)
_ChromosomeComponent
(in
Bio.Graphics.BasicChromosome
)
_select_charged()
(in
IsoelectricPoint
)
__init__()
(in
Motif
)
_CircularDrawer
(in
Bio.Graphics.GenomeDiagram
)
_seq_topologies
(in
Bio.SeqIO.XdnaIO
)
__init__()
(in
Record
)
_CKDTree
(in
Bio.KDTree
)
_seq_types
(in
Bio.SeqIO.XdnaIO
)
__init__()
(in
XXmotifCommandline
)
_clade_complex_types
(in
Parser
)
_SeqIO_to_alignment_iterator()
(in
Bio.AlignIO
)
__init__()
(in
Motif
)
_clade_list_types
(in
Parser
)
_seqmatrix2strmatrix()
(in
Bio.Nexus.Nexus
)
__init__()
(in
Record
)
_clade_to_bitstr()
(in
Bio.Phylo.Consensus
)
_sequence_line()
(in
Record
)
__init__()
(in
JASPAR5
)
_clade_tracked_tags
(in
Parser
)
_serialize()
(in
Bio.Phylo.PhyloXMLIO
)
__init__()
(in
Record
)
_class_matcher()
(in
Bio.Phylo.BaseTree
)
_set()
(in
Nexus
)
__init__()
(in
GenericPositionMatrix
)
_classify_alphabet_for_nexus()
(in
NexusWriter
)
_set_a()
(in
ColorSpiral
)
__init__()
(in
PositionWeightMatrix
)
_classname()
(in
Record
)
_set_b()
(in
ColorSpiral
)
__init__()
(in
Instance
)
_clean()
(in
Bio.SeqIO.Interfaces
)
_set_color()
(in
Clade
)
__init__()
(in
Motif
)
_clean_alignments()
(in
Bio.pairwise2
)
_set_colors_and_shapes()
(in
ComparativeScatterPlot
)
__init__()
(in
Record
)
_clean_attrib()
(in
Bio.Phylo.PhyloXMLIO
)
_set_confidence()
(in
Clade
)
__init__()
(in
Record
)
_clean_blocks()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
_set_confidence()
(in
Phylogeny
)
__init__()
(in
ScoreDistribution
)
_clean_location()
(in
_BaseGenBankConsumer
)
_set_frame()
(in
Bio.SearchIO.ExonerateIO._base
)
__init__()
(in
Record
)
_clean_translation()
(in
FeatureValueCleaner
)
_set_header_application()
(in
BlastParser
)
__init__()
(in
XMSScanner
)
_cleaner
(in
Bio.GenBank
)
_set_header_database()
(in
BlastParser
)
__init__()
(in
affine_penalty
)
_clear()
(in
QCPSuperimposer
)
_set_header_query()
(in
BlastParser
)
__init__()
(in
dictionary_match
)
_clear()
(in
SVDSuperimposer
)
_set_header_query_id()
(in
BlastParser
)
__init__()
(in
identity_match
)
_clear_parameter()
(in
AbstractCommandline
)
_set_header_query_letters()
(in
BlastParser
)
__init__()
(in
JsonWriter
)
_ClustalOmega
(in
Bio.Align.Applications
)
_set_header_reference()
(in
BlastParser
)
__init__()
(in
PlateRecord
)
_Clustalw
(in
Bio.Align.Applications
)
_set_header_version()
(in
BlastParser
)
__init__()
(in
WellRecord
)
_cluster
(in
Bio.Cluster
)
_set_hsp_align_len()
(in
BlastParser
)
__init__()
(in
DBSeq
)
_CMDLINE_DNAL
(in
Bio.Wise.dnal
)
_set_hsp_bit_score()
(in
BlastParser
)
__init__()
(in
DBSeqRecord
)
_CMDLINE_FGREP_COUNT
(in
Bio.Wise.dnal
)
_set_hsp_e_value()
(in
BlastParser
)
__init__()
(in
Adaptor
)
_CMDLINE_PSW
(in
Bio.Wise.psw
)
_set_hsp_gaps()
(in
BlastParser
)
__init__()
(in
BioSeqDatabase
)
_codeset()
(in
Nexus
)
_set_hsp_hit_frame()
(in
BlastParser
)
__init__()
(in
DBServer
)
_codonposset()
(in
Nexus
)
_set_hsp_hit_from()
(in
BlastParser
)
__init__()
(in
_CursorWrapper
)
_codons2re()
(in
Bio.codonalign
)
_set_hsp_hit_strand()
(in
BlastParser
)
__init__()
(in
Generic_dbutils
)
_cofactor()
(in
Record
)
_set_hsp_hit_to()
(in
BlastParser
)
__init__()
(in
DatabaseLoader
)
_col_ave()
(in
Bio.NMR.NOEtools
)
_set_hsp_identity()
(in
BlastParser
)
__init__()
(in
DatabaseRemover
)
_collapse_wspace()
(in
Bio.Phylo.PhyloXMLIO
)
_set_hsp_midline()
(in
BlastParser
)
__int__()
(in
Confidence
)
_color_from_count()
(in
ChromosomeCounts
)
_set_hsp_positive()
(in
BlastParser
)
__iter__()
(in
MultipleSeqAlignment
)
_color_trans
(in
Bio.Graphics.BasicChromosome
)
_set_hsp_query_end()
(in
BlastParser
)
__iter__()
(in
PairwiseAlignments
)
_Colors
(in
Bio.Graphics.GenomeDiagram
)
_set_hsp_query_frame()
(in
BlastParser
)
__iter__()
(in
AlignmentIterator
)
_COLUMN_FRAG
(in
Bio.SearchIO.BlastIO.blast_tab
)
_set_hsp_query_seq()
(in
BlastParser
)
__iter__()
(in
UndoHandle
)
_COLUMN_HIT
(in
Bio.SearchIO.BlastIO.blast_tab
)
_set_hsp_query_start()
(in
BlastParser
)
__iter__()
(in
_IndexedSeqFileDict
)
_COLUMN_HSP
(in
Bio.SearchIO.BlastIO.blast_tab
)
_set_hsp_query_strand()
(in
BlastParser
)
__iter__()
(in
_IndexedSeqFileProxy
)
_COLUMN_QRESULT
(in
Bio.SearchIO.BlastIO.blast_tab
)
_set_hsp_score()
(in
BlastParser
)
__iter__()
(in
_SQLiteManySeqFilesDict
)
_combine_args()
(in
Bio.Phylo.BaseTree
)
_set_hsp_seqs()
(in
Bio.SearchIO.FastaIO
)
__iter__()
(in
Iterator
)
_combine_matchers()
(in
Bio.Phylo.BaseTree
)
_set_hsp_subject_seq()
(in
BlastParser
)
__iter__()
(in
StandardData
)
_comment()
(in
Record
)
_set_jitter()
(in
ColorSpiral
)
__iter__()
(in
AbstractPropertyMap
)
_comment_line()
(in
Record
)
_set_kind()
(in
AlignmentColumn
)
__iter__()
(in
DisorderedAtom
)
_comp_coords()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
_set_location_operator()
(in
SeqFeature
)
__iter__()
(in
DisorderedEntityWrapper
)
_comp_intron_lens()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
_set_parameters_expect()
(in
BlastParser
)
__iter__()
(in
Entity
)
_comp_split_codons()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
_set_parameters_filter()
(in
BlastParser
)
__iter__()
(in
Clade
)
_compact4nexus()
(in
Bio.Nexus.Nexus
)
_set_parameters_gap_extend()
(in
BlastParser
)
__iter__()
(in
Events
)
_complex_location
(in
Bio.GenBank
)
_set_parameters_gap_penalties()
(in
BlastParser
)
__iter__()
(in
Other
)
_compute_gapopen_num()
(in
Bio.SearchIO.BlastIO.blast_tab
)
_set_parameters_matrix()
(in
BlastParser
)
__iter__()
(in
Phyloxml
)
_consensus_alphabet()
(in
Bio.Alphabet
)
_set_parameters_sc_match()
(in
BlastParser
)
__iter__()
(in
_FileIterator
)
_consensus_base_alphabet()
(in
Bio.Alphabet
)
_set_parameters_sc_mismatch()
(in
BlastParser
)
__iter__()
(in
BlastTabIndexer
)
_consrtm_line()
(in
Reference
)
_set_per_column_annotations()
(in
MultipleSeqAlignment
)
__iter__()
(in
BlastTabParser
)
_construct_cgi()
(in
Bio.Entrez
)
_set_per_letter_annotations()
(in
SeqRecord
)
__iter__()
(in
BlastTextParser
)
_construct_params()
(in
Bio.Entrez
)
_set_qresult_hits()
(in
Bio.SearchIO.FastaIO
)
__iter__()
(in
BlastXmlIndexer
)
_consume_entry()
(in
BlastTableReader
)
_set_record_hits()
(in
BlastParser
)
__iter__()
(in
BlastXmlParser
)
_consume_header()
(in
BlastTableReader
)
_set_record_query_def()
(in
BlastParser
)
__iter__()
(in
BlatPslIndexer
)
_contents()
(in
Bio.NaiveBayes
)
_set_record_query_id()
(in
BlastParser
)
__iter__()
(in
BlatPslParser
)
_contig_line()
(in
Record
)
_set_record_query_letters()
(in
BlastParser
)
__iter__()
(in
_BaseExonerateIndexer
)
_convert
(in
Bio.SeqIO
)
_set_ref()
(in
SeqFeature
)
__iter__()
(in
_BaseExonerateParser
)
_convert_formats
(in
Bio.TogoWS
)
_set_ref_db()
(in
SeqFeature
)
__iter__()
(in
FastaM10Indexer
)
_convert_key()
(in
Array
)
_set_rel_paths()
(in
Paml
)
__iter__()
(in
FastaM10Parser
)
_convert_list()
(in
_CursorWrapper
)
_set_rel_paths()
(in
Baseml
)
__iter__()
(in
Hhsuite2TextParser
)
_convert_to_python_numbers()
(in
_BaseGenBankConsumer
)
_set_rel_paths()
(in
Codeml
)
__iter__()
(in
Hmmer2TextIndexer
)
_convert_tuple()
(in
_CursorWrapper
)
_set_seq()
(in
HSPFragment
)
__iter__()
(in
Hmmer2TextParser
)
_converter
(in
Bio.SeqIO._convert
)
_set_seq()
(in
SeqRecord
)
__iter__()
(in
Hmmer3TabIndexer
)
_copy_and_check()
(in
Bio.MarkovModel
)
_set_statistics_db_len()
(in
BlastParser
)
__iter__()
(in
Hmmer3TabParser
)
_correct_matrix()
(in
SeqMat
)
_set_statistics_db_num()
(in
BlastParser
)
__iter__()
(in
Hmmer3TextIndexer
)
_count_clades()
(in
Bio.Phylo.Consensus
)
_set_statistics_eff_space()
(in
BlastParser
)
__iter__()
(in
Hmmer3TextParser
)
_count_codons()
(in
CodonAdaptationIndex
)
_set_statistics_entropy()
(in
BlastParser
)
__iter__()
(in
InterproscanXmlParser
)
_count_diff_NG86()
(in
Bio.codonalign.codonseq
)
_set_statistics_hsp_len()
(in
BlastParser
)
__iter__()
(in
Iterator
)
_count_diff_YN00()
(in
Bio.codonalign.codonseq
)
_set_statistics_kappa()
(in
BlastParser
)
__iter__()
(in
Hit
)
_count_emissions()
(in
KnownStateTrainer
)
_set_statistics_lambda()
(in
BlastParser
)
__iter__()
(in
HSP
)
_count_replacement()
(in
Bio.codonalign.codonalignment
)
_set_strand()
(in
CompoundLocation
)
__iter__()
(in
QueryResult
)
_count_site_NG86()
(in
Bio.codonalign.codonseq
)
_set_strand()
(in
FeatureLocation
)
__iter__()
(in
CompoundLocation
)
_count_site_YN00()
(in
Bio.codonalign.codonseq
)
_set_strand()
(in
SeqFeature
)
__iter__()
(in
FeatureLocation
)
_count_transitions()
(in
KnownStateTrainer
)
_set_taxonomy()
(in
Clade
)
__iter__()
(in
SeqFeature
)
_create_hits()
(in
Hmmer3TextParser
)
_set_v_final()
(in
ColorSpiral
)
__iter__()
(in
SequenceIterator
)
_create_hsp()
(in
Bio.SearchIO.BlatIO
)
_set_v_init()
(in
ColorSpiral
)
__iter__()
(in
XMLRecordIterator
)
_create_hsp()
(in
Bio.SearchIO.ExonerateIO._base
)
_set_zero_diagonal()
(in
DistanceMatrix
)
__iter__()
(in
_PacketIterator
)
_create_qresult()
(in
Hhsuite2TextParser
)
_setbgcolor()
(in
Graphics
)
__iter__()
(in
EmblRandomAccess
)
_CrossLink
(in
Bio.Graphics.GenomeDiagram
)
_setcoords()
(in
Graphics
)
__iter__()
(in
FastqRandomAccess
)
_csvData
(in
Bio.phenotype.phen_micro
)
_setentry1()
(in
Relation
)
__iter__()
(in
GenBankRandomAccess
)
_current_track_start_end()
(in
AbstractDrawer
)
_setentry2()
(in
Relation
)
__iter__()
(in
IntelliGeneticsRandomAccess
)
_CursorWrapper
(in
BioSQL.BioSeqDatabase
)
_setfgcolor()
(in
Graphics
)
__iter__()
(in
SequentialSeqFileRandomAccess
)
_data_map()
(in
Bio.NMR.NOEtools
)
_setheight()
(in
Graphics
)
__iter__()
(in
SffRandomAccess
)
_DatabaseReportConsumer
(in
Bio.SearchIO._legacy.NCBIStandalone
)
_setid()
(in
Component
)
__iter__()
(in
SwissRandomAccess
)
_datafile
(in
Bio.phenotype.phen_micro
)
_setid()
(in
Entry
)
__iter__()
(in
TabRandomAccess
)
_db_source_line()
(in
Record
)
_setid()
(in
Reaction
)
__iter__()
(in
UniprotRandomAccess
)
_dblink_line()
(in
Record
)
_setname()
(in
Entry
)
__iter__()
(in
SeqRecord
)
_dblinks()
(in
Record
)
_setname()
(in
Pathway
)
__iter__()
(in
BgzfReader
)
_dblinks()
(in
Record
)
_setnames()
(in
Reaction
)
__iter__()
(in
PlateRecord
)
_dblinks()
(in
Record
)
_setnumber()
(in
Pathway
)
__iter__()
(in
WellRecord
)
_dbutils
(in
BioSQL.DBUtils
)
_setreaction()
(in
Entry
)
__iter__()
(in
BioSeqDatabase
)
_decode()
(in
Bio.SeqIO.SnapGeneIO
)
_setup_blast_v1()
(in
BlastParser
)
__iter__()
(in
DBServer
)
_DEFAULT_FIELDS
(in
Bio.SearchIO.BlastIO.blast_tab
)
_setup_blast_v2()
(in
BlastParser
)
__le__()
(in
PairwiseAlignment
)
_default_wrap()
(in
Bio.KEGG
)
_setupTime
(in
Bio.phenotype.phen_micro
)
__le__()
(in
Atom
)
_definition()
(in
Record
)
_setwidth()
(in
Graphics
)
__le__()
(in
Chain
)
_definition_line()
(in
Record
)
_setx()
(in
Graphics
)
__le__()
(in
DisorderedEntityWrapper
)
_del_confidence()
(in
Clade
)
_sety()
(in
Graphics
)
__le__()
(in
Entity
)
_del_confidence()
(in
Phylogeny
)
_sff
(in
Bio.SeqIO.SffIO
)
__le__()
(in
Confidence
)
_delbgcolor()
(in
Graphics
)
_sff_do_slow_index()
(in
Bio.SeqIO.SffIO
)
__le__()
(in
RestrictionType
)
_delcoords()
(in
Graphics
)
_sff_file_header()
(in
Bio.SeqIO.SffIO
)
__le__()
(in
MutableSeq
)
_delentry1()
(in
Relation
)
_sff_find_roche_index()
(in
Bio.SeqIO.SffIO
)
__le__()
(in
Seq
)
_delentry2()
(in
Relation
)
_sff_read_raw_record()
(in
Bio.SeqIO.SffIO
)
__le___()
(in
SeqRecord
)
_delfgcolor()
(in
Graphics
)
_sff_read_roche_index()
(in
Bio.SeqIO.SffIO
)
__len__()
(in
MultipleSeqAlignment
)
_delheight()
(in
Graphics
)
_sff_read_seq_record()
(in
Bio.SeqIO.SffIO
)
__len__()
(in
PairwiseAlignments
)
_delid()
(in
Component
)
_SffTrimIterator()
(in
Bio.SeqIO.SffIO
)
__len__()
(in
MafIndex
)
_delid()
(in
Entry
)
_ShelveIndex
(in
Bio.Index
)
__len__()
(in
Chain
)
_delid()
(in
Reaction
)
_ShelveIndex__version
(in
_ShelveIndex
)
__len__()
(in
Crystal
)
_delname()
(in
Entry
)
_ShelveIndex__version_key
(in
_ShelveIndex
)
__len__()
(in
Hetero
)
_delname()
(in
Pathway
)
_shift()
(in
AfterPosition
)
__len__()
(in
Primers
)
_delnames()
(in
Reaction
)
_shift()
(in
BeforePosition
)
__len__()
(in
fff_rec
)
_delnumber()
(in
Pathway
)
_shift()
(in
BetweenPosition
)
__len__()
(in
_IndexedSeqFileDict
)
_delreaction()
(in
Entry
)
_shift()
(in
CompoundLocation
)
__len__()
(in
_SQLiteManySeqFilesDict
)
_delwidth()
(in
Graphics
)
_shift()
(in
ExactPosition
)
__len__()
(in
AbstractDrawer
)
_delx()
(in
Graphics
)
_shift()
(in
FeatureLocation
)
__len__()
(in
FeatureSet
)
_dely()
(in
Graphics
)
_shift()
(in
OneOfPosition
)
__len__()
(in
GraphData
)
_DescriptionConsumer
(in
Bio.SearchIO._legacy.NCBIStandalone
)
_shift()
(in
SeqFeature
)
__len__()
(in
GraphSet
)
_determine_position()
(in
BarChartDistribution
)
_shift()
(in
UnknownPosition
)
__len__()
(in
StandardData
)
_diagnose_error()
(in
BlastErrorParser
)
_shift()
(in
WithinPosition
)
__len__()
(in
AbstractPropertyMap
)
_Diagram
(in
Bio.Graphics.GenomeDiagram
)
_simple_location
(in
Bio.GenBank
)
__len__()
(in
DisorderedEntityWrapper
)
_Dialign
(in
Bio.Align.Applications
)
_solexa_to_illumina_quality_str
(in
Bio.SeqIO.QualityIO
)
__len__()
(in
Entity
)
_dict_str2bool()
(in
Bio.Phylo.PhyloXMLIO
)
_solexa_to_sanger_quality_str
(in
Bio.SeqIO.QualityIO
)
__len__()
(in
Fragment
)
_diff_codon()
(in
Bio.codonalign.codonseq
)
_solexa_to_solexa_quality_str
(in
Bio.SeqIO.QualityIO
)
__len__()
(in
Clade
)
_digest()
(in
CAPSMap
)
_solo_bond
(in
Bio.GenBank
)
__len__()
(in
Events
)
_digest_with()
(in
CAPSMap
)
_solo_location
(in
Bio.GenBank
)
__len__()
(in
Phyloxml
)
_dijkstra()
(in
Bio.codonalign.codonalignment
)
_sort_keys_by_values()
(in
Bio.Nexus.Nexus
)
__len__()
(in
_Matrix
)
_dimensions()
(in
Nexus
)
_sorted_attrs()
(in
Bio.Phylo.BaseTree
)
__len__()
(in
FormattedSeq
)
_DIRFMT
(in
Bio.SeqIO.AbiIO
)
_source_line()
(in
Record
)
__len__()
(in
RestrictionType
)
_disease()
(in
Record
)
_split_accessions()
(in
_BaseGenBankConsumer
)
__len__()
(in
Hit
)
_dna_complement_table
(in
Bio.Seq
)
_split_contig()
(in
_InsdcWriter
)
__len__()
(in
HSP
)
_domain_re
(in
Bio.SCOP
)
_split_fragment()
(in
Bio.SearchIO.ExonerateIO._base
)
__len__()
(in
HSPFragment
)
_draw_arc()
(in
CircularDrawer
)
_split_id()
(in
PhylipIterator
)
__len__()
(in
QueryResult
)
_draw_arc_arrow()
(in
CircularDrawer
)
_split_id()
(in
RelaxedPhylipIterator
)
__len__()
(in
MutableSeq
)
_draw_arc_line()
(in
CircularDrawer
)
_split_keywords()
(in
_BaseGenBankConsumer
)
__len__()
(in
Seq
)
_draw_arc_poly()
(in
CircularDrawer
)
_split_multi_line()
(in
_InsdcWriter
)
__len__()
(in
UnknownSeq
)
_draw_distributions()
(in
DistributionPage
)
_split_namespace()
(in
Bio.Phylo.PhyloXMLIO
)
__len__()
(in
CompoundLocation
)
_draw_label()
(in
Chromosome
)
_split_reference_locations()
(in
_FeatureConsumer
)
__len__()
(in
FeatureLocation
)
_draw_label()
(in
ChromosomeSegment
)
_split_taxonomy()
(in
_BaseGenBankConsumer
)
__len__()
(in
SeqFeature
)
_draw_labels()
(in
Chromosome
)
_splitline()
(in
MMCIF2Dict
)
__len__()
(in
SeqRecord
)
_draw_legend()
(in
Organism
)
_spring_layout()
(in
Bio.Graphics.BasicChromosome
)
__len__()
(in
Motif
)
_draw_legend()
(in
DistributionPage
)
_SQLiteManySeqFilesDict
(in
Bio.File
)
__len__()
(in
PlateRecord
)
_draw_scatter_plot()
(in
ComparativeScatterPlot
)
_srt
(in
Bio.SeqIO.SffIO
)
__len__()
(in
WellRecord
)
_draw_segment()
(in
ChromosomeSegment
)
_start_blast_record()
(in
BlastParser
)
__len__()
(in
DBSeq
)
_draw_segment()
(in
TelomereSegment
)
_start_hit()
(in
BlastParser
)
__len__()
(in
BioSeqDatabase
)
_draw_sigil_arrow()
(in
CircularDrawer
)
_start_hit_descr_item()
(in
BlastParser
)
__len__()
(in
DBServer
)
_draw_sigil_arrow()
(in
LinearDrawer
)
_start_hsp()
(in
BlastParser
)
__long__()
(in
Confidence
)
_draw_sigil_big_arrow()
(in
CircularDrawer
)
_STATE_CONS_BLOCK
(in
Bio.SearchIO.FastaIO
)
__lt__()
(in
PairwiseAlignment
)
_draw_sigil_big_arrow()
(in
LinearDrawer
)
_STATE_HIT_BLOCK
(in
Bio.SearchIO.FastaIO
)
__lt__()
(in
Atom
)
_draw_sigil_box()
(in
CircularDrawer
)
_STATE_NONE
(in
Bio.SearchIO.FastaIO
)
__lt__()
(in
Chain
)
_draw_sigil_box()
(in
LinearDrawer
)
_STATE_QUERY_BLOCK
(in
Bio.SearchIO.FastaIO
)
__lt__()
(in
DisorderedEntityWrapper
)
_draw_sigil_cut_corner_box()
(in
CircularDrawer
)
_statelabels()
(in
Nexus
)
__lt__()
(in
Entity
)
_draw_sigil_jaggy()
(in
CircularDrawer
)
_stateset()
(in
Nexus
)
__lt__()
(in
Confidence
)
_draw_sigil_jaggy()
(in
LinearDrawer
)
_StaticArgument
(in
Bio.Application
)
__lt__()
(in
RestrictionType
)
_draw_sigil_octo()
(in
LinearDrawer
)
_stitch_rows()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
__lt__()
(in
MutableSeq
)
_draw_subcomponents()
(in
ChromosomeSegment
)
_str2bool()
(in
Bio.Phylo.PhyloXMLIO
)
__lt__()
(in
Seq
)
_draw_title()
(in
Organism
)
_str_aln()
(in
HSPFragment
)
__lt__()
(in
SeqRecord
)
_draw_title()
(in
ComparativeScatterPlot
)
_str_hsp_header()
(in
_BaseHSP
)
__maf_indexer()
(in
MafIndex
)
_draw_title()
(in
BarChartDistribution
)
_str_line()
(in
MultipleSeqAlignment
)
__make_diagram()
(in
Bio.motifs.mast
)
_draw_title()
(in
DistributionPage
)
_strainName
(in
Bio.phenotype.phen_micro
)
__make_new_index()
(in
MafIndex
)
_drop()
(in
Ambiguous
)
_strainNumber
(in
Bio.phenotype.phen_micro
)
__marker
(in
QueryResult
)
_drop()
(in
Defined
)
_strainType
(in
Bio.phenotype.phen_micro
)
__mod__()
(in
Confidence
)
_drop()
(in
NotDefined
)
_STRAND_MAP
(in
Bio.SearchIO.ExonerateIO._base
)
__mod__()
(in
RestrictionType
)
_dssp_cys
(in
Bio.PDB.DSSP'
)
_string_as_base_36()
(in
Bio.SeqIO.SffIO
)
__mul__()
(in
Vector
)
_DTD_OPT
(in
Bio.SearchIO.BlastIO.blast_xml
)
_string_matcher()
(in
Bio.Phylo.BaseTree
)
__mul__()
(in
Confidence
)
_effector()
(in
Record
)
_string_to_bytes()
(in
Bio._py3k
)
__mul__()
(in
MutableSeq
)
_elem_AAseq()
(in
SeqXmlIterator
)
_stroke_and_fill_colors()
(in
Bio.Graphics.GenomeDiagram._AbstractDrawer
)
__mul__()
(in
Seq
)
_elem_description()
(in
SeqXmlIterator
)
_struct_wrap()
(in
Bio.KEGG
)
__mul__()
(in
UnknownSeq
)
_elem_DNAseq()
(in
SeqXmlIterator
)
_structures()
(in
Record
)
__mul__()
(in
SeqMat
)
_ELEM_FRAG
(in
Bio.SearchIO.BlastIO.blast_xml
)
_structures()
(in
Record
)
__mul__()
(in
DBSeq
)
_ELEM_FRAG
(in
Bio.SearchIO.InterproscanIO.interproscan_xml
)
_sub_clade()
(in
Bio.Phylo.Consensus
)
__ne__()
(in
PairwiseAlignment
)
_ELEM_HIT
(in
Bio.SearchIO.BlastIO.blast_xml
)
_sub_placeholder()
(in
Sqlite_dbutils
)
__ne__()
(in
Chain
)
_ELEM_HIT
(in
Bio.SearchIO.InterproscanIO.interproscan_xml
)
_sub_set()
(in
Analysis
)
__ne__()
(in
Hetero
)
_ELEM_HSP
(in
Bio.SearchIO.BlastIO.blast_xml
)
_substrate()
(in
Record
)
__ne__()
(in
NoneElement
)
_ELEM_HSP
(in
Bio.SearchIO.InterproscanIO.interproscan_xml
)
_SUPPORTED_FIELDS
(in
Bio.SearchIO.BlastIO.blast_tab
)
__ne__()
(in
Atom
)
_ELEM_META
(in
Bio.SearchIO.BlastIO.blast_xml
)
_Switch
(in
Bio.Application
)
__ne__()
(in
Entity
)
_ELEM_QRESULT_FALLBACK
(in
Bio.SearchIO.BlastIO.blast_xml
)
_sysname()
(in
Record
)
__ne__()
(in
Reaction
)
_ELEM_QRESULT_OPT
(in
Bio.SearchIO.BlastIO.blast_xml
)
_table_h
(in
Bio.SeqUtils.CheckSum
)
__ne__()
(in
Graph
)
_elem_RNAseq()
(in
SeqXmlIterator
)
_taxlabels()
(in
Nexus
)
__ne__()
(in
MultiGraph
)
_eliminate()
(in
Nexus
)
_taxpartition()
(in
Nexus
)
__ne__()
(in
Confidence
)
_embl_convert_fasta()
(in
Bio.SeqIO._convert
)
_taxset()
(in
Nexus
)
__ne__()
(in
RestrictionType
)
_EmbossCommandLine
(in
Bio.Emboss.Applications
)
_TCoffee
(in
Bio.Align.Applications
)
__ne__()
(in
MutableSeq
)
_EmbossMinimalCommandLine
(in
Bio.Emboss.Applications
)
_test()
(in
Bio.Application
)
__ne__()
(in
Seq
)
_empty_bytes_string
(in
Bio.SearchIO.BlastIO.blast_xml
)
_test()
(in
Bio.Blast.Applications
)
__ne__()
(in
CompoundLocation
)
_empty_DNA
(in
Bio.Restriction.Restriction
)
_test()
(in
Bio.Seq
)
__ne__()
(in
FeatureLocation
)
_encode_options()
(in
Bio.Entrez
)
_test()
(in
Bio.Wise
)
__ne__()
(in
Reference
)
_end_blast_record()
(in
BlastParser
)
_test()
(in
Bio.Wise.dnal
)
__ne__()
(in
SeqRecord
)
_end_description_accession()
(in
BlastParser
)
_test()
(in
Bio.Wise.psw
)
__ne__()
(in
PlateRecord
)
_end_description_id()
(in
BlastParser
)
_test_dist()
(in
PPBuilder
)
__ne__()
(in
WellRecord
)
_end_description_sciname()
(in
BlastParser
)
_test_equivalence()
(in
StructureAlignment
)
__neg__()
(in
Vector
)
_end_description_taxid()
(in
BlastParser
)
_test_global_hz_both()
(in
GenePopController
)
__neg__()
(in
Confidence
)
_end_description_title()
(in
BlastParser
)
_test_normal()
(in
Analysis
)
__new__()
(in
Array
)
_end_hit()
(in
BlastParser
)
_test_pop_hz_both()
(in
GenePopController
)
__new__()
(in
IntegerElement
)
_end_hit_descr_item()
(in
BlastParser
)
_test_reverse()
(in
Analysis
)
__new__()
(in
StringElement
)
_end_hsp()
(in
BlastParser
)
_time_denominators
(in
Bio.SeqIO.SffIO
)
__new__()
(in
UnicodeElement
)
_END_OF_FILE_MARKER
(in
Bio.SearchIO.HHsuiteIO.hhsuite2_text
)
_title()
(in
Nexus
)
__new__()
(in
_BitString
)
_entry()
(in
Record
)
_title_line()
(in
Reference
)
__new__()
(in
AfterPosition
)
_entry()
(in
Record
)
_tokenize()
(in
MMCIF2Dict
)
__new__()
(in
BeforePosition
)
_entry()
(in
Record
)
_toobj()
(in
_InMemoryIndex
)
__new__()
(in
BetweenPosition
)
_entry_db_fields
(in
Bio.TogoWS
)
_toOPM()
(in
Bio.phenotype.phen_micro
)
__new__()
(in
ExactPosition
)
_entry_db_formats
(in
Bio.TogoWS
)
_tostr()
(in
_InMemoryIndex
)
__new__()
(in
OneOfPosition
)
_entry_db_names
(in
Bio.TogoWS
)
_Track
(in
Bio.Graphics.GenomeDiagram
)
__new__()
(in
WithinPosition
)
_enzyme()
(in
Record
)
_trackA()
(in
CrossLink
)
__next__()
(in
PairwiseAlignments
)
_eof()
(in
_Scanner
)
_trackB()
(in
CrossLink
)
__next__()
(in
ClustalIterator
)
_equal_topology()
(in
Bio.Phylo.Consensus
)
_train_iis()
(in
Bio.MaxEntropy
)
__next__()
(in
EmbossIterator
)
_escape_filename()
(in
Bio.Application
)
_transfer_attrs()
(in
_BaseSearchObject
)
__next__()
(in
AlignmentIterator
)
_eval_feature_fn()
(in
Bio.MaxEntropy
)
_translate()
(in
Nexus
)
__next__()
(in
MauveIterator
)
_exp_freq_table_from_obs_freq()
(in
Bio.SubsMat
)
_translate_id()
(in
AbstractAtomPropertyMap
)
__next__()
(in
MsfIterator
)
_exp_logsum()
(in
Bio.MarkovModel
)
_translate_id()
(in
AbstractPropertyMap
)
__next__()
(in
PhylipIterator
)
_EXTRACT
(in
Bio.SeqIO.AbiIO
)
_translate_id()
(in
AbstractResiduePropertyMap
)
__next__()
(in
SequentialPhylipIterator
)
_extract_alignment_region()
(in
Bio.AlignIO.FastaIO
)
_translate_id()
(in
Chain
)
__next__()
(in
StockholmIterator
)
_extract_ids_and_descs()
(in
Bio.SearchIO.BlastIO.blast_xml
)
_translate_str()
(in
Bio.Seq
)
__next__()
(in
BlastTableReader
)
_fails_conditions()
(in
Bio.SearchIO._legacy.ParserSupport
)
_tree()
(in
Nexus
)
__next__()
(in
UndoHandle
)
_fastq_convert_fasta()
(in
Bio.SeqIO._convert
)
_tree_to_bitstrs()
(in
Bio.Phylo.Consensus
)
__next__()
(in
Iterator
)
_fastq_convert_qual()
(in
Bio.SeqIO._convert
)
_treepartition()
(in
Nexus
)
__next__()
(in
CharBuffer
)
_fastq_convert_tab()
(in
Bio.SeqIO._convert
)
_treeset()
(in
Nexus
)
__next__()
(in
StandardData
)
_fastq_generic()
(in
Bio.SeqIO._convert
)
_ucscbin()
(in
MafIndex
)
__next__()
(in
_FileIterator
)
_fastq_generic2()
(in
Bio.SeqIO._convert
)
_ungap()
(in
Bio.Alphabet
)
__next__()
(in
Iterator
)
_fastq_illumina_convert_fastq_illumina()
(in
Bio.SeqIO._convert
)
_unhandled()
(in
_BaseGenBankConsumer
)
__next__()
(in
SequenceIterator
)
_fastq_illumina_convert_fastq_sanger()
(in
Bio.SeqIO._convert
)
_unhandled()
(in
AbstractConsumer
)
__next__()
(in
_PacketIterator
)
_fastq_illumina_convert_fastq_solexa()
(in
Bio.SeqIO._convert
)
_unhandled_section()
(in
AbstractConsumer
)
__next__()
(in
BgzfReader
)
_fastq_illumina_convert_qual()
(in
Bio.SeqIO._convert
)
_uniform_norm()
(in
Bio.MarkovModel
)
__next_section()
(in
PrintFormat
)
_fastq_sanger_convert_fastq_illumina()
(in
Bio.SeqIO._convert
)
_unique_label()
(in
Bio.Nexus.Nexus
)
__nonzero__()
(in
CompoundLocation
)
_fastq_sanger_convert_fastq_sanger()
(in
Bio.SeqIO._convert
)
_universal_read_mode
(in
Bio._py3k
)
__nonzero__()
(in
FeatureLocation
)
_fastq_sanger_convert_fastq_solexa()
(in
Bio.SeqIO._convert
)
_unknown_nexus_block()
(in
Nexus
)
__or__()
(in
_BitString
)
_fastq_sanger_convert_qual()
(in
Bio.SeqIO._convert
)
_update()
(in
PlateRecord
)
__package__
(in
Bio.Affy.CelFile
)
_fastq_solexa_convert_fastq_illumina()
(in
Bio.SeqIO._convert
)
_update_ecitmatch_variables()
(in
Bio.Entrez
)
__package__
(in
Bio.Affy
)
_fastq_solexa_convert_fastq_sanger()
(in
Bio.SeqIO._convert
)
_update_left_right_taxon_values()
(in
DatabaseLoader
)
__package__
(in
Bio.Align.AlignInfo
)
_fastq_solexa_convert_fastq_solexa()
(in
Bio.SeqIO._convert
)
_update_pKs_tables()
(in
IsoelectricPoint
)
__package__
(in
Bio.Align.Applications._ClustalOmega
)
_fastq_solexa_convert_qual()
(in
Bio.SeqIO._convert
)
_upper()
(in
Alphabet
)
__package__
(in
Bio.Align.Applications._Clustalw
)
_Fasttree
(in
Bio.Phylo.Applications
)
_upper()
(in
AlphabetEncoder
)
__package__
(in
Bio.Align.Applications._Dialign
)
_Feature
(in
Bio.Graphics.GenomeDiagram
)
_upper()
(in
Gapped
)
__package__
(in
Bio.Align.Applications._MSAProbs
)
_FeatureConsumer
_upper()
(in
HasStopCodon
)
__package__
(in
Bio.Align.Applications._Mafft
)
_features_line()
(in
Record
)
_upper()
(in
ThreeLetterProtein
)
__package__
(in
Bio.Align.Applications._Muscle
)
_FeatureSet
(in
Bio.Graphics.GenomeDiagram
)
_utils
(in
Bio.Phylo
)
__package__
(in
Bio.Align.Applications._Prank
)
_feed_feature_table()
(in
InsdcScanner
)
_utils
(in
Bio.SearchIO
)
__package__
(in
Bio.Align.Applications._Probcons
)
_feed_first_line()
(in
EmblScanner
)
_utils
(in
Bio
)
__package__
(in
Bio.Align.Applications._TCoffee
)
_feed_first_line()
(in
GenBankScanner
)
_utree()
(in
Nexus
)
__package__
(in
Bio.Align.Applications
)
_feed_first_line()
(in
InsdcScanner
)
_valid_UAN_read_name
(in
Bio.SeqIO.SffIO
)
__package__
(in
Bio.Align
)
_feed_first_line()
(in
_ImgtScanner
)
_validate()
(in
AbstractCommandline
)
__package__
(in
Bio.Align._aligners
)
_feed_first_line_new()
(in
EmblScanner
)
_validate()
(in
NcbiblastformatterCommandline
)
__package__
(in
Bio.Align.substitution_matrices
)
_feed_first_line_old()
(in
EmblScanner
)
_validate()
(in
NcbiblastnCommandline
)
__package__
(in
Bio.AlignIO.ClustalIO
)
_feed_first_line_patents()
(in
EmblScanner
)
_validate()
(in
NcbimakeblastdbCommandline
)
__package__
(in
Bio.AlignIO.EmbossIO
)
_feed_first_line_patents_kipo()
(in
EmblScanner
)
_validate()
(in
NcbipsiblastCommandline
)
__package__
(in
Bio.AlignIO.FastaIO
)
_feed_header_lines()
(in
EmblScanner
)
_validate()
(in
NcbirpsblastCommandline
)
__package__
(in
Bio.AlignIO.Interfaces
)
_feed_header_lines()
(in
GenBankScanner
)
_validate()
(in
_Ncbiblast2SeqCommandline
)
__package__
(in
Bio.AlignIO.MafIO
)
_feed_header_lines()
(in
InsdcScanner
)
_validate()
(in
_NcbiblastCommandline
)
__package__
(in
Bio.AlignIO.MauveIO
)
_feed_misc_lines()
(in
EmblScanner
)
_validate()
(in
_NcbiblastMain2SeqCommandline
)
__package__
(in
Bio.AlignIO.MsfIO
)
_feed_misc_lines()
(in
GenBankScanner
)
_validate()
(in
SeqretCommandline
)
__package__
(in
Bio.AlignIO.NexusIO
)
_feed_misc_lines()
(in
InsdcScanner
)
_validate()
(in
_EmbossCommandLine
)
__package__
(in
Bio.AlignIO.PhylipIO
)
_feed_seq_length()
(in
EmblScanner
)
_validate_cols()
(in
BlatPslParser
)
__package__
(in
Bio.AlignIO.StockholmIO
)
_fetch_counts_matrix()
(in
JASPAR5
)
_validate_fragment()
(in
HSP
)
__package__
(in
Bio.AlignIO
)
_fetch_internal_id()
(in
JASPAR5
)
_validate_hsp()
(in
Hit
)
__package__
(in
Bio.Alphabet.IUPAC
)
_fetch_internal_id_list()
(in
JASPAR5
)
_validate_incompatibilities()
(in
_NcbibaseblastCommandline
)
__package__
(in
Bio.Alphabet.Reduced
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_fetch_latest_version()
(in
JASPAR5
)
_verify_alphabet()
(in
Bio.Alphabet
)
__package__
(in
Bio.Alphabet
)
_fetch_motif_by_internal_id()
(in
JASPAR5
)
_version_line()
(in
Record
)
__package__
(in
Bio.Application
)
_fgrep_count()
(in
Bio.Wise.dnal
)
_viterbi()
(in
Bio.MarkovModel
)
__package__
(in
Bio.Blast.Applications
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_file
(in
Bio.phenotype.phen_micro
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_walk()
(in
Tree
)
__package__
(in
Bio.Blast.NCBIWWW
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_FileIterator
(in
Bio.PopGen.GenePop.Controller
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_weight_list()
(in
ProteinAnalysis
)
__package__
(in
Bio.Blast.NCBIXML
)
_filter_search()
(in
TreeMixin
)
_wgs_line()
(in
Record
)
__package__
(in
Bio.Blast.ParseBlastTable
)
_find_gap_open()
(in
Bio.pairwise2
)
_wgs_scafld_line()
(in
Record
)
__package__
(in
Bio.Blast.Record
)
_find_min_max()
(in
ComparativeScatterPlot
)
_within_location
(in
Bio.GenBank
)
__package__
(in
Bio.Blast
)
_find_start()
(in
Bio.pairwise2
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_within_position
(in
Bio.GenBank
)
__package__
(in
Bio.CAPS
)
_find_start_entry()
(in
Bio.NMR.xpktools
)
_wrap_kegg()
(in
Bio.KEGG
)
__package__
(in
Bio.Cluster
)
_finish_backtrace()
(in
Bio.pairwise2
)
_wrap_location()
(in
_InsdcWriter
)
__package__
(in
Bio.Cluster._cluster
)
_first_defined()
(in
Bio.Graphics.GenomeDiagram._Diagram
)
_wrapped_genbank()
(in
Bio.GenBank.Record
)
__package__
(in
Bio.Compass
)
_fix_name_class()
(in
DatabaseLoader
)
_write()
(in
Bio.Graphics
)
__package__
(in
Bio.Crystal
)
_flag
(in
Bio.SeqIO.SffIO
)
_write_block()
(in
BgzfWriter
)
__package__
(in
Bio.Data.CodonTable
)
_flip()
(in
AfterPosition
)
_write_comment()
(in
EmblWriter
)
__package__
(in
Bio.Data.IUPACData
)
_flip()
(in
BeforePosition
)
_write_comment()
(in
GenBankWriter
)
__package__
(in
Bio.Data.SCOPData
)
_flip()
(in
BetweenPosition
)
_write_contig()
(in
EmblWriter
)
__package__
(in
Bio.Data
)
_flip()
(in
CompoundLocation
)
_write_contig()
(in
GenBankWriter
)
__package__
(in
Bio.Emboss.Applications
)
_flip()
(in
ExactPosition
)
_write_dbxrefs()
(in
SeqXmlWriter
)
__package__
(in
Bio.Emboss.Primer3
)
_flip()
(in
FeatureLocation
)
_write_description()
(in
SeqXmlWriter
)
__package__
(in
Bio.Emboss.PrimerSearch
)
_flip()
(in
OneOfPosition
)
_write_elem_block()
(in
BlastXmlWriter
)
__package__
(in
Bio.Emboss
)
_flip()
(in
SeqFeature
)
_write_feature()
(in
_InsdcWriter
)
__package__
(in
Bio.Entrez.Parser
)
_flip()
(in
UnknownPosition
)
_write_feature_qualifier()
(in
_InsdcWriter
)
__package__
(in
Bio.Entrez
)
_flip()
(in
WithinPosition
)
_write_hits()
(in
BlastXmlWriter
)
__package__
(in
Bio.ExPASy.Enzyme
)
_flip_codons()
(in
Bio.SearchIO.ExonerateIO.exonerate_text
)
_write_hsps()
(in
BlastXmlWriter
)
__package__
(in
Bio.ExPASy.Prodoc
)
_float()
(in
Bio.Phylo.PhyloXMLIO
)
_write_index()
(in
SffWriter
)
__package__
(in
Bio.ExPASy.Prosite
)
_force_alphabet()
(in
Bio.AlignIO
)
_write_kegg()
(in
Bio.KEGG
)
__package__
(in
Bio.ExPASy.ScanProsite
)
_force_alphabet()
(in
Bio.SeqIO
)
_write_keywords()
(in
EmblWriter
)
__package__
(in
Bio.ExPASy
)
_format()
(in
Nexus
)
_WRITE_MAPS
(in
Bio.SearchIO.BlastIO.blast_xml
)
__package__
(in
Bio.ExPASy.cellosaurus
)
_format_1D()
(in
Array
)
_write_multi_entries()
(in
GenBankWriter
)
__package__
(in
Bio.FSSP.FSSPTools
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_format_2D()
(in
Array
)
_write_multi_line()
(in
EmblWriter
)
__package__
(in
Bio.FSSP
)
_format_comment()
(in
Bio.Phylo.NewickIO
)
_write_multi_line()
(in
GenBankWriter
)
__package__
(in
Bio.FSSP.fssp_rec
)
_format_date()
(in
Bio.PDB.parse_pdb_header'
)
_write_param()
(in
BlastXmlWriter
)
__package__
(in
Bio.File
)
_format_generalized()
(in
PairwiseAlignment
)
_write_preamble()
(in
BlastXmlWriter
)
__package__
(in
Bio.GenBank.Record
)
_format_mmcif_col()
(in
MMCIFIO
)
_write_properties()
(in
SeqXmlWriter
)
__package__
(in
Bio.GenBank.Scanner
)
_format_psl()
(in
PairwiseAlignment
)
_write_pstring()
(in
XdnaWriter
)
__package__
(in
Bio.GenBank
)
_FormatToIterator
(in
Bio.AlignIO
)
_write_qresults()
(in
BlastXmlWriter
)
__package__
(in
Bio.GenBank.utils
)
_FormatToIterator
(in
Bio.SeqIO
)
_write_record()
(in
MafWriter
)
__package__
(in
Bio.Geo.Record
)
_FormatToIterator
(in
Bio.phenotype
)
_write_record()
(in
MauveWriter
)
__package__
(in
Bio.Geo
)
_FormatToRandomAccess
(in
Bio.SeqIO._index
)
_write_record()
(in
StockholmWriter
)
__package__
(in
Bio.Graphics.BasicChromosome
)
_FormatToString
(in
Bio.SeqIO
)
_write_references()
(in
EmblWriter
)
__package__
(in
Bio.Graphics.ColorSpiral
)
_FormatToWriter
(in
Bio.AlignIO
)
_write_references()
(in
GenBankWriter
)
__package__
(in
Bio.Graphics.Comparative
)
_FormatToWriter
(in
Bio.SeqIO
)
_write_seq()
(in
SeqXmlWriter
)
__package__
(in
Bio.Graphics.DisplayRepresentation
)
_FormatToWriter
(in
Bio.phenotype
)
_write_sequence()
(in
EmblWriter
)
__package__
(in
Bio.Graphics.Distribution
)
_formula()
(in
Record
)
_write_sequence()
(in
GenBankWriter
)
__package__
(in
Bio.Graphics.GenomeDiagram._AbstractDrawer
)
_forward()
(in
Bio.MarkovModel
)
_write_single_line()
(in
EmblWriter
)
__package__
(in
Bio.Graphics.GenomeDiagram._CircularDrawer
)
_forward_recursion()
(in
AbstractDPAlgorithms
)
_write_single_line()
(in
GenBankWriter
)
__package__
(in
Bio.Graphics.GenomeDiagram._Colors
)
_forward_recursion()
(in
ScaledDPAlgorithms
)
_write_species()
(in
SeqXmlWriter
)
__package__
(in
Bio.Graphics.GenomeDiagram._CrossLink
)
_FRAGMENT_FILE
(in
Bio.PDB.FragmentMapper'
)
_write_the_first_line()
(in
GenBankWriter
)
__package__
(in
Bio.Graphics.GenomeDiagram._Diagram
)
_fragment_re
(in
Bio.SCOP.Residues
)
_write_the_first_lines()
(in
EmblWriter
)
__package__
(in
Bio.Graphics.GenomeDiagram._Feature
)
_freq_from_count()
(in
FreqTable
)
_write_tree()
(in
Writer
)
__package__
(in
Bio.Graphics.GenomeDiagram._FeatureSet
)
_full_to_half()
(in
SeqMat
)
_WRITER_MAP
(in
Bio.SearchIO
)
__package__
(in
Bio.Graphics.GenomeDiagram._Graph
)
_function_matcher()
(in
Bio.Phylo.BaseTree
)
_XMLparser
(in
Bio.Blast.NCBIXML
)
__package__
(in
Bio.Graphics.GenomeDiagram._GraphSet
)
_G_test()
(in
Bio.codonalign.codonalignment
)
_xxmotif
(in
Bio.motifs.applications
)
__package__
(in
Bio.Graphics.GenomeDiagram._LinearDrawer
)
_gaf10byproteiniterator()
(in
Bio.UniProt.GOA
)
_yn00()
(in
Bio.codonalign.codonseq
)
__package__
(in
Bio.Graphics.GenomeDiagram._Track
)
_gaf10iterator()
(in
Bio.UniProt.GOA
)
__package__
(in
Bio.Graphics.GenomeDiagram
)
_gaf20byproteiniterator()
(in
Bio.UniProt.GOA
)
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