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_
__add__()
(in
Chain
)
__mod__()
(in
RestrictionType
)
_drop()
(in
NotDefined
)
__add__()
(in
Location
)
__mul__()
(in
Vector
)
_dssp_cys
(in
Bio.PDB.DSSP'
)
__add__()
(in
Vector
)
__mul__()
(in
SeqMat
)
_dump()
(in
Bio.Parsers.spark
)
__add__()
(in
RestrictionBatch
)
__ne__()
(in
Chain
)
_effector()
(in
Record
)
__add__()
(in
RestrictionType
)
__ne__()
(in
Hetero
)
_eliminate()
(in
Nexus
)
__add__()
(in
SeqMap
)
__ne__()
(in
Reaction
)
_embl_convert_fasta()
(in
Bio.SeqIO._convert
)
__add__()
(in
MutableSeq
)
__ne__()
(in
Graph
)
_EmbossCommandLine
(in
Bio.Emboss.Applications
)
__add__()
(in
Seq
)
__ne__()
(in
HashSet
)
_EmbossMinimalCommandLine
(in
Bio.Emboss.Applications
)
__add__()
(in
UnknownSeq
)
__ne__()
(in
MultiGraph
)
_end_BlastOutput_db()
(in
BlastParser
)
__add__()
(in
SeqMat
)
__ne__()
(in
RestrictionType
)
_end_BlastOutput_hits()
(in
BlastParser
)
__add__()
(in
DBSeq
)
__neg__()
(in
Vector
)
_end_BlastOutput_program()
(in
BlastParser
)
__call__()
(in
CelParser
)
__next_section()
(in
PrintFormat
)
_end_BlastOutput_query_def()
(in
BlastParser
)
__call__()
(in
affine_penalty
)
__nonzero__()
(in
SeqRecord
)
_end_BlastOutput_query_ID()
(in
BlastParser
)
__call__()
(in
dictionary_match
)
__package__
(in
Bio.Affy.CelFile
)
_end_BlastOutput_query_len()
(in
BlastParser
)
__call__()
(in
identity_match
)
__package__
(in
Bio.Affy
)
_end_BlastOutput_reference()
(in
BlastParser
)
__cmp__()
(in
HasStopCodon
)
__package__
(in
Bio.Align.AlignInfo
)
_end_BlastOutput_version()
(in
BlastParser
)
__cmp__()
(in
Organism
)
__package__
(in
Bio.Align.Applications._Clustalw
)
_end_Hit()
(in
BlastParser
)
__cmp__()
(in
Integer
)
__package__
(in
Bio.Align.Applications._Dialign
)
_end_Hit_accession()
(in
BlastParser
)
__cmp__()
(in
Symbol
)
__package__
(in
Bio.Align.Applications._Mafft
)
_end_Hit_def()
(in
BlastParser
)
__cmp__()
(in
Token
)
__package__
(in
Bio.Align.Applications._Muscle
)
_end_Hit_id()
(in
BlastParser
)
__cmp__()
(in
MutableSeq
)
__package__
(in
Bio.Align.Applications._Prank
)
_end_Hit_len()
(in
BlastParser
)
__cmp__()
(in
AbstractPosition
)
__package__
(in
Bio.Align.Applications._Probcons
)
_end_Hsp_align_len()
(in
BlastParser
)
__contains__()
(in
Chain
)
__package__
(in
Bio.Align.Applications._TCoffee
)
_end_Hsp_bit_score()
(in
BlastParser
)
__contains__()
(in
HashSet
)
__package__
(in
Bio.Align.Applications
)
_end_Hsp_evalue()
(in
BlastParser
)
__contains__()
(in
RestrictionBatch
)
__package__
(in
Bio.Align.FormatConvert
)
_end_Hsp_gaps()
(in
BlastParser
)
__contains__()
(in
Seq
)
__package__
(in
Bio.Align.Generic
)
_end_Hsp_hit_frame()
(in
BlastParser
)
__contains__()
(in
SeqRecord
)
__package__
(in
Bio.Align
)
_end_Hsp_hit_from()
(in
BlastParser
)
__del__()
(in
TempFile
)
__package__
(in
Bio.AlignAce.AlignAceStandalone
)
_end_Hsp_hit_to()
(in
BlastParser
)
__del__()
(in
_InMemoryIndex
)
__package__
(in
Bio.AlignAce.Applications
)
_end_Hsp_hseq()
(in
BlastParser
)
__del__()
(in
_ShelveIndex
)
__package__
(in
Bio.AlignAce.CompareAceStandalone
)
_end_Hsp_identity()
(in
BlastParser
)
__del__()
(in
_FileIterator
)
__package__
(in
Bio.AlignAce.Motif
)
_end_Hsp_midline()
(in
BlastParser
)
__del__()
(in
RebaseUpdate
)
__package__
(in
Bio.AlignAce.Parser
)
_end_Hsp_positive()
(in
BlastParser
)
__del_annotations()
(in
DBSeqRecord
)
__package__
(in
Bio.AlignAce.Scanner
)
_end_Hsp_qseq()
(in
BlastParser
)
__del_dbxrefs()
(in
DBSeqRecord
)
__package__
(in
Bio.AlignAce
)
_end_Hsp_query_frame()
(in
BlastParser
)
__del_features()
(in
DBSeqRecord
)
__package__
(in
Bio.AlignIO.ClustalIO
)
_end_Hsp_query_from()
(in
BlastParser
)
__del_seq()
(in
DBSeqRecord
)
__package__
(in
Bio.AlignIO.EmbossIO
)
_end_Hsp_query_to()
(in
BlastParser
)
__delitem__()
(in
Chain
)
__package__
(in
Bio.AlignIO.FastaIO
)
_end_Hsp_score()
(in
BlastParser
)
__delitem__()
(in
Crystal
)
__package__
(in
Bio.AlignIO.Interfaces
)
_end_Iteration()
(in
BlastParser
)
__delitem__()
(in
_InMemoryIndex
)
__package__
(in
Bio.AlignIO.NexusIO
)
_end_Iteration_query_def()
(in
BlastParser
)
__delitem__()
(in
Chain
)
__package__
(in
Bio.AlignIO.PhylipIO
)
_end_Iteration_query_ID()
(in
BlastParser
)
__delitem__()
(in
MutableSeq
)
__package__
(in
Bio.AlignIO.StockholmIO
)
_end_Iteration_query_len()
(in
BlastParser
)
__delslice__()
(in
Chain
)
__package__
(in
Bio.AlignIO
)
_end_Parameters_expect()
(in
BlastParser
)
__div__()
(in
Vector
)
__package__
(in
Bio.Alphabet.IUPAC
)
_end_Parameters_filter()
(in
BlastParser
)
__div__()
(in
RestrictionBatch
)
__package__
(in
Bio.Alphabet.Reduced
)
_end_Parameters_gap_extend()
(in
BlastParser
)
__div__()
(in
RestrictionType
)
__package__
(in
Bio.Alphabet
)
_end_Parameters_gap_open()
(in
BlastParser
)
__doc__
(in
Bio.PDB.AbstractPropertyMap
)
__package__
(in
Bio.Application
)
_end_Parameters_matrix()
(in
BlastParser
)
__doc__
(in
Bio.PDB.Atom
)
__package__
(in
Bio.Blast.Applications
)
_end_Parameters_sc_match()
(in
BlastParser
)
__doc__
(in
Bio.PDB.Chain
)
__package__
(in
Bio.Blast.NCBIStandalone
)
_end_Parameters_sc_mismatch()
(in
BlastParser
)
__doc__
(in
Bio.PDB.Entity
)
__package__
(in
Bio.Blast.NCBIWWW
)
_end_Statistics_db_len()
(in
BlastParser
)
__doc__
(in
Bio.PDB.HSExposure
)
__package__
(in
Bio.Blast.NCBIXML
)
_end_Statistics_db_num()
(in
BlastParser
)
__doc__
(in
Bio.PDB.MMCIF2Dict
)
__package__
(in
Bio.Blast.ParseBlastTable
)
_end_Statistics_eff_space()
(in
BlastParser
)
__doc__
(in
Bio.PDB.MMCIFParser
)
__package__
(in
Bio.Blast.Record
)
_end_Statistics_entropy()
(in
BlastParser
)
__doc__
(in
Bio.PDB.Model
)
__package__
(in
Bio.Blast
)
_end_Statistics_hsp_len()
(in
BlastParser
)
__doc__
(in
Bio.PDB.NACCESS
)
__package__
(in
Bio.CAPS
)
_end_Statistics_kappa()
(in
BlastParser
)
__doc__
(in
Bio.PDB.NeighborSearch
)
__package__
(in
Bio.Clustalw
)
_end_Statistics_lambda()
(in
BlastParser
)
__doc__
(in
Bio.PDB.PDBExceptions
)
__package__
(in
Bio.Compass
)
_entry()
(in
Record
)
__doc__
(in
Bio.PDB.Polypeptide
)
__package__
(in
Bio.Crystal
)
_entry()
(in
Record
)
__doc__
(in
Bio.PDB.Residue
)
__package__
(in
Bio.Data.CodonTable
)
_enzyme()
(in
Record
)
__doc__
(in
Bio.PDB.Selection
)
__package__
(in
Bio.Data.IUPACData
)
_EOF
(in
GenericParser
)
__doc__
(in
Bio.PDB.Structure
)
__package__
(in
Bio.Data
)
_escape_filename()
(in
Bio.Application
)
__doc__
(in
Bio.PDB.StructureBuilder
)
__package__
(in
Bio.EZRetrieve
)
_eval_feature_fn()
(in
Bio.MaxEntropy
)
__doc__
(in
Bio.PDB
)
__package__
(in
Bio.Emboss.Applications
)
_evalue()
(in
MEMEMotif
)
__enter__()
(in
UndoHandle
)
__package__
(in
Bio.Emboss.Primer3
)
_evalue()
(in
MEMEMotif
)
__eq__()
(in
Chain
)
__package__
(in
Bio.Emboss.PrimerSearch
)
_exp_freq_table_from_obs_freq()
(in
Bio.SubsMat
)
__eq__()
(in
Hetero
)
__package__
(in
Bio.Emboss
)
_exp_logsum()
(in
Bio.MarkovModel
)
__eq__()
(in
Reaction
)
__package__
(in
Bio.Encodings.IUPACEncoding
)
_extract_alignment_region()
(in
FastaM10Iterator
)
__eq__()
(in
Graph
)
__package__
(in
Bio.Encodings
)
_extract_pattern_hits()
(in
Bio.Prosite
)
__eq__()
(in
HashSet
)
__package__
(in
Bio.Entrez.Parser
)
_fails_conditions()
(in
Bio.ParserSupport
)
__eq__()
(in
MultiGraph
)
__package__
(in
Bio.Entrez
)
_fastq_convert_fasta()
(in
Bio.SeqIO._convert
)
__eq__()
(in
FormattedSeq
)
__package__
(in
Bio.Enzyme
)
_fastq_convert_tab()
(in
Bio.SeqIO._convert
)
__eq__()
(in
RestrictionType
)
__package__
(in
Bio.ExPASy.Enzyme
)
_fastq_generic()
(in
Bio.SeqIO._convert
)
__exit__()
(in
UndoHandle
)
__package__
(in
Bio.ExPASy.Prodoc
)
_fastq_generic2()
(in
Bio.SeqIO._convert
)
__filename_key
(in
Dictionary
)
__package__
(in
Bio.ExPASy.Prosite
)
_fastq_illumina_convert_fastq_illumina()
(in
Bio.SeqIO._convert
)
__filename_key
(in
Dictionary
)
__package__
(in
Bio.ExPASy.ScanProsite
)
_fastq_illumina_convert_fastq_sanger()
(in
Bio.SeqIO._convert
)
__filename_key
(in
Dictionary
)
__package__
(in
Bio.ExPASy
)
_fastq_illumina_convert_fastq_solexa()
(in
Bio.SeqIO._convert
)
__floordiv__()
(in
RestrictionType
)
__package__
(in
Bio.FSSP.FSSPTools
)
_fastq_sanger_convert_fastq_illumina()
(in
Bio.SeqIO._convert
)
__format__()
(in
Alignment
)
__package__
(in
Bio.FSSP
)
_fastq_sanger_convert_fastq_sanger()
(in
Bio.SeqIO._convert
)
__format__()
(in
SeqRecord
)
__package__
(in
Bio.FSSP.fssp_rec
)
_fastq_sanger_convert_fastq_solexa()
(in
Bio.SeqIO._convert
)
__ge__()
(in
RestrictionType
)
__package__
(in
Bio.Fasta.FastaAlign
)
_fastq_solexa_convert_fastq_illumina()
(in
Bio.SeqIO._convert
)
__get_annotations()
(in
DBSeqRecord
)
__package__
(in
Bio.Fasta
)
_fastq_solexa_convert_fastq_sanger()
(in
Bio.SeqIO._convert
)
__get_dbxrefs()
(in
DBSeqRecord
)
__package__
(in
Bio.File
)
_fastq_solexa_convert_fastq_solexa()
(in
Bio.SeqIO._convert
)
__get_features()
(in
DBSeqRecord
)
__package__
(in
Bio.FilteredReader
)
_FastqSeqFileDict
(in
Bio.SeqIO._index
)
__get_seq()
(in
DBSeqRecord
)
__package__
(in
Bio.GA.Crossover.General
)
_Feature
(in
Bio.Graphics.GenomeDiagram
)
__getattr__()
(in
AlphabetEncoder
)
__package__
(in
Bio.GA.Crossover.GeneralPoint
)
_FeatureConsumer
__getattr__()
(in
AmbiguousCodonTable
)
__package__
(in
Bio.GA.Crossover.Point
)
_features_line()
(in
Record
)
__getattr__()
(in
QueryRow
)
__package__
(in
Bio.GA.Crossover.TwoPoint
)
_FeatureSet
(in
Bio.Graphics.GenomeDiagram
)
__getattr__()
(in
SGMLHandle
)
__package__
(in
Bio.GA.Crossover.Uniform
)
_feed_feature_table()
(in
InsdcScanner
)
__getattr__()
(in
UndoHandle
)
__package__
(in
Bio.GA.Crossover
)
_feed_first_line()
(in
EmblScanner
)
__getattr__()
(in
FilteredReader
)
__package__
(in
Bio.GA.Evolver
)
_feed_first_line()
(in
GenBankScanner
)
__getattr__()
(in
Surrogate
)
__package__
(in
Bio.GA.Mutation.General
)
_feed_first_line()
(in
InsdcScanner
)
__getattr__()
(in
Feature
)
__package__
(in
Bio.GA.Mutation.Simple
)
_feed_first_line_new()
(in
EmblScanner
)
__getattr__()
(in
DisorderedEntityWrapper
)
__package__
(in
Bio.GA.Mutation
)
_feed_first_line_old()
(in
EmblScanner
)
__getattr__()
(in
AbstractConsumer
)
__package__
(in
Bio.GA.Organism
)
_feed_header_lines()
(in
EmblScanner
)
__getattr__()
(in
SGMLStrippingConsumer
)
__package__
(in
Bio.GA.Repair.Stabilizing
)
_feed_header_lines()
(in
GenBankScanner
)
__getattr__()
(in
TaggingConsumer
)
__package__
(in
Bio.GA.Repair
)
_feed_header_lines()
(in
InsdcScanner
)
__getattr__()
(in
Dictionary
)
__package__
(in
Bio.GA.Selection.Abstract
)
_feed_misc_lines()
(in
EmblScanner
)
__getattr__()
(in
Prosite
)
__package__
(in
Bio.GA.Selection.Diversity
)
_feed_misc_lines()
(in
GenBankScanner
)
__getattr__()
(in
Dictionary
)
__package__
(in
Bio.GA.Selection.RouletteWheel
)
_feed_misc_lines()
(in
InsdcScanner
)
__getattr__()
(in
_SeqLength
)
__package__
(in
Bio.GA.Selection.Tournament
)
_feed_seq_length()
(in
EmblScanner
)
__getattr__()
(in
Dictionary
)
__package__
(in
Bio.GA.Selection
)
_fgrep_count()
(in
Bio.Wise.dnal
)
__getitem__()
(in
PSSM
)
__package__
(in
Bio.GA
)
_FileIterator
(in
Bio.PopGen.GenePop.Controller
)
__getitem__()
(in
Alignment
)
__package__
(in
Bio.GenBank.LocationParser
)
_find_global_start()
(in
Bio.pairwise2
)
__getitem__()
(in
Chain
)
__package__
(in
Bio.GenBank.Record
)
_find_local_start()
(in
Bio.pairwise2
)
__getitem__()
(in
Crystal
)
__package__
(in
Bio.GenBank.Scanner
)
_find_min_max()
(in
ComparativeScatterPlot
)
__getitem__()
(in
AmbiguousForwardTable
)
__package__
(in
Bio.GenBank
)
_find_start()
(in
Bio.pairwise2
)
__getitem__()
(in
fff_rec
)
__package__
(in
Bio.GenBank.utils
)
_find_start_entry()
(in
Bio.NMR.xpktools
)
__getitem__()
(in
ForgivingDictionary
)
__package__
(in
Bio.Geo.Record
)
_fitness_cmp()
(in
TournamentSelection
)
__getitem__()
(in
FeatureDict
)
__package__
(in
Bio.Geo
)
_fix_name_class()
(in
DatabaseLoader
)
__getitem__()
(in
NCBIDictionary
)
__package__
(in
Bio.Graphics.BasicChromosome
)
_fix_varsplic_sequences()
(in
_RecordConsumer
)
__getitem__()
(in
Diagram
)
__package__
(in
Bio.Graphics.Comparative
)
_flush_text()
(in
InterProParser
)
__getitem__()
(in
FeatureSet
)
__package__
(in
Bio.Graphics.DisplayRepresentation
)
_flush_text()
(in
NdbParser
)
__getitem__()
(in
GraphData
)
__package__
(in
Bio.Graphics.Distribution
)
_force_alphabet()
(in
Bio.AlignIO
)
__getitem__()
(in
GraphSet
)
__package__
(in
Bio.Graphics.GenomeDiagram._AbstractDrawer
)
_force_alphabet()
(in
Bio.SeqIO
)
__getitem__()
(in
Track
)
__package__
(in
Bio.Graphics.GenomeDiagram._CircularDrawer
)
_format()
(in
Nexus
)
__getitem__()
(in
Motif
)
__package__
(in
Bio.Graphics.GenomeDiagram._Colors
)
_format_date()
(in
Bio.PDB.parse_pdb_header'
)
__getitem__()
(in
AbstractPropertyMap
)
__package__
(in
Bio.Graphics.GenomeDiagram._Diagram
)
_FormatToIndexedDict
(in
Bio.SeqIO._index
)
__getitem__()
(in
Chain
)
__package__
(in
Bio.Graphics.GenomeDiagram._Feature
)
_FormatToIterator
(in
Bio.AlignIO
)
__getitem__()
(in
Entity
)
__package__
(in
Bio.Graphics.GenomeDiagram._FeatureSet
)
_FormatToIterator
(in
Bio.SeqIO
)
__getitem__()
(in
FragmentMapper
)
__package__
(in
Bio.Graphics.GenomeDiagram._Graph
)
_FormatToWriter
(in
Bio.AlignIO
)
__getitem__()
(in
MMCIF2Dict
)
__package__
(in
Bio.Graphics.GenomeDiagram._GraphSet
)
_FormatToWriter
(in
Bio.SeqIO
)
__getitem__()
(in
Vector
)
__package__
(in
Bio.Graphics.GenomeDiagram._LinearDrawer
)
_formula()
(in
Record
)
__getitem__()
(in
CreateDict
)
__package__
(in
Bio.Graphics.GenomeDiagram._Track
)
_forward()
(in
Bio.MarkovModel
)
__getitem__()
(in
Dictionary
)
__package__
(in
Bio.Graphics.GenomeDiagram
)
_forward_recursion()
(in
ScaledDPAlgorithms
)
__getitem__()
(in
Prosite
)
__package__
(in
Bio.Graphics
)
_foward_recursion()
(in
AbstractDPAlgorithms
)
__getitem__()
(in
PrositeMatch
)
__package__
(in
Bio.HMM.DynamicProgramming
)
_FRAGMENT_FILE
(in
Bio.PDB.FragmentMapper'
)
__getitem__()
(in
Dictionary
)
__package__
(in
Bio.HMM.MarkovModel
)
_fragment_re
(in
Bio.SCOP.Residues'
)
__getitem__()
(in
Dictionary
)
__package__
(in
Bio.HMM.Trainer
)
_freq_from_count()
(in
FreqTable
)
__getitem__()
(in
FormattedSeq
)
__package__
(in
Bio.HMM.Utilities
)
_from_horiz_matrix()
(in
Motif
)
__getitem__()
(in
Index
)
__package__
(in
Bio.HMM
)
_from_jaspar_pfm()
(in
Motif
)
__getitem__()
(in
FileIndex
)
__package__
(in
Bio.HotRand
)
_from_jaspar_sites()
(in
Motif
)
__getitem__()
(in
defaultdict
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Bio.InterPro
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Bio.Motif
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SeqMat
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Bio.KEGG.Map
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Bio.PopGen.SimCoal.Template
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Bio.PopGen.GenePop.Controller
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SeqRecord
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Bio.MEME.Motif
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FDistController
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Bio.MEME.Parser
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Bio.MEME
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Bio.MarkovModel
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TwoCrossover
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DBServer
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Bio.MaxEntropy
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Record
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Bio.Medline
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SummaryInfo
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fff_rec
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Bio.Motif.Applications._AlignAce
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GenBankWriter
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Bio.Motif.Applications
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Bio.Motif.Parsers.AlignAce
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PDBIO
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Bio.Alphabet
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SeqMap
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Bio.Motif.Parsers
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Bio.Motif.Thresholds
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SummaryInfo
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Bio.Motif._Motif
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SummaryInfo
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Bio.Motif
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DatabaseLoader
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Reaction
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Bio.NMR.NOEtools
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HSExposureCA
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Chain
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Bio.NMR
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HSExposureCB
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RestrictionBatch
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Bio.NMR.xpktools
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Bio.Blast.NCBIStandalone
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SeqMap
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Bio.NaiveBayes
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SummaryInfo
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Bio.Ndb
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Bio.Wise.dnal
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CelConsumer
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Bio.NetCatch
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DatabaseLoader
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CelParser
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Bio.NeuralNetwork.BackPropagation.Layer
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CelRecord
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Bio.NeuralNetwork.BackPropagation.Network
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PDBParser
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Record
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Bio.NeuralNetwork.BackPropagation
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MMCIFParser
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PSSM
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Bio.NeuralNetwork.Gene.Motif
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Chain
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SummaryInfo
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Bio.NeuralNetwork.Gene.Pattern
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Bio.SeqIO.QualityIO
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ClustalwCommandline
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Bio.NeuralNetwork.Gene.Schema
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Nexus
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DialignCommandline
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Bio.NeuralNetwork.Gene.Signature
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Bio.PDB.parse_pdb_header'
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MafftCommandline
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Bio.NeuralNetwork.Gene
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FilteredReader
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MuscleCommandline
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Bio.NeuralNetwork.StopTraining
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SummaryInfo
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PrankCommandline
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Bio.NeuralNetwork.Training
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_FeatureConsumer
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ProbconsCommandline
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Bio.NeuralNetwork
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StockholmIterator
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TCoffeeCommandline
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Bio.Nexus.Nexus
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MotifFinder
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FormatConverter
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Bio.Nexus.Nodes
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DiversitySelection
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Alignment
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Bio.Nexus.Trees
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Nexus
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AlignAceCommandline
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Bio.Nexus
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FeatureLocation
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CompareAceCommandline
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Bio.PDB.AbstractPropertyMap
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FeatureLocation
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Motif
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Bio.PDB.Atom
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SchemaFactory
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AlignAceConsumer
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Bio.PDB.Chain
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DatabaseLoader
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AlignAceParser
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Bio.PDB.DSSP'
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GenePopController
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CompareAceConsumer
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Bio.PDB.Dice
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AbstractCommandline
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CompareAceParser
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Bio.PDB.Entity
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FDistController
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AlignmentIterator
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Bio.PDB.FragmentMapper'
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Bio.SeqIO.QualityIO
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AlignmentWriter
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Bio.PDB.HSExposure
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_FeatureConsumer
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SequentialAlignmentWriter
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Bio.PDB.Model
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Bio.PDB.parse_pdb_header'
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AlphabetEncoder
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Bio.PDB.NACCESS
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Bio.SeqIO.QualityIO
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Gapped
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Bio.PDB.PDBExceptions
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Seq
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HasStopCodon
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Bio.PDB.PDBIO'
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SequenceWriter
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AbstractCommandline
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Bio.PDB.PDBList'
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DatabaseLoader
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ApplicationResult
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Bio.PDB.PDBParser'
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SignatureFinder
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_AbstractParameter
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Bio.PDB.PSEA
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_RecordConsumer
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_Argument
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Bio.PDB.Polypeptide
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Bio.SeqIO.QualityIO
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_Option
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Bio.PDB.Residue
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DatabaseLoader
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_Switch
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Bio.PDB.ResidueDepth'
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DatabaseLoader
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BlastallCommandline
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Bio.PDB.Selection
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DatabaseLoader
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BlastpgpCommandline
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Bio.PDB.Structure
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FDistController
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FastacmdCommandline
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Bio.PDB.StructureAlignment'
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DatabaseLoader
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RpsBlastCommandline
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Bio.PDB.StructureBuilder
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NeighborSearch
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_BlastAllOrPgpCommandLine
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Bio.PDB.Superimposer'
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SchemaFactory
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_BlastCommandLine
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Bio.PDB.Vector'
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Tree
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BlastErrorParser
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Bio.PDB
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Bio.PopGen.GenePop.Controller
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BlastParser
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Bio.PDB.mmCIF
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Bio.PopGen.GenePop.Controller
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Iterator
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Bio.PDB.parse_pdb_header'
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Bio.Graphics.GenomeDiagram
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PSIBlastParser
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Bio.ParserSupport
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Bio.Graphics.GenomeDiagram
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_BlastConsumer
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Bio.Parsers
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SummaryInfo
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_BlastErrorConsumer
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Bio.Parsers.spark
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Bio.SeqIO._convert
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_PSIBlastConsumer
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Bio.Pathway.Rep.Graph
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PDBParser
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BlastParser
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Bio.Pathway.Rep.HashSet
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Bio.Blast.NCBIStandalone
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_XMLparser
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Bio.Pathway.Rep.MultiGraph
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Bio.Blast.NCBIStandalone
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BlastTableEntry
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Bio.Pathway.Rep
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Bio.PopGen.GenePop.Controller
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BlastTableReader
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Bio.Pathway
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Bio.PDB.Dice
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BlastTableRec
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Bio.PopGen.Async.Local
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StockholmIterator
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Alignment
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Bio.PopGen.Async
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Bio.MaxEntropy
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Blast
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Bio.PopGen.FDist.Async
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Bio.GenBank.Record
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DatabaseReport
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Bio.PopGen.FDist.Controller
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Bio.SeqIO
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Description
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Bio.PopGen.FDist.Utils
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ScoreDistribution
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HSP
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Bio.PopGen.FDist
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Bio.SeqIO._index
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Header
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Bio.PopGen.GenePop.Controller
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Record
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MultipleAlignment
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Bio.PopGen.GenePop.EasyController
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ProtsimLine
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PSIBlast
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Bio.PopGen.GenePop.Utils
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STSLine
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Parameters
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Bio.PopGen.GenePop
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SequenceLine
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Round
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Bio.PopGen.SimCoal.Async
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UnigeneProtsimRecord
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CAPSMap
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Bio.PopGen.SimCoal.Cache
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UnigeneSTSRecord
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DifferentialCutsite
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Bio.PopGen.SimCoal.Controller
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UnigeneSequenceRecord
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ClustalAlignment
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Bio.PopGen.SimCoal.Template
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Bio.SeqUtils.CheckSum
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MultipleAlignCL
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Bio.PopGen.SimCoal
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SeqMat
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Record
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Bio.PopGen
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Bio.Index
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Iterator
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Bio.PropertyManager
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_InMemoryIndex
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Record
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Bio.Prosite.Pattern
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_InMemoryIndex
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RecordParser
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Bio.Prosite.Prodoc
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Bio.SeqIO.InsdcIO
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_Consumer
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Bio.Prosite
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Bio.SeqIO.InsdcIO
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Chain
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Bio.PubMed
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Bio.SeqIO.InsdcIO
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Crystal
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Bio.SCOP.Cla
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DatabaseLoader
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Hetero
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Bio.SCOP.Des
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Bio.Blast.NCBIStandalone
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AmbiguousCodonTable
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Bio.SCOP.Dom
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StructureBuilder
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AmbiguousForwardTable
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Bio.SCOP.FileIndex
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CaPPBuilder
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CodonTable
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Bio.SCOP.Hie
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PPBuilder
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NCBICodonTable
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Bio.SCOP.Raf
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PhylipIterator
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Create
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Bio.SCOP.Residues'
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Bio.SeqIO
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Insert
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Bio.SCOP
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Location
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IterationCursor
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Bio.SVDSuperimposer.SVDSuperimposer'
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Reference
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Query
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Bio.SVDSuperimposer
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Record
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QueryAll
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Bio.Search
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Bio.Nexus.Nexus
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QueryGeneric
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Bio.Seq
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Instance
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QueryRow
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Bio.SeqFeature
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Motif
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QuerySingle
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Bio.SeqIO.AceIO
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MEMEInstance
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DiffseqCommandline
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Bio.SeqIO.FastaIO
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Bio.Graphics.GenomeDiagram
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EConsenseCommandline
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Bio.SeqIO.IgIO
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DatabaseLoader
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EInvertedCommandline
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Bio.SeqIO.InsdcIO
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DatabaseLoader
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ENeighborCommandline
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Bio.SeqIO.Interfaces
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DatabaseLoader
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EProtDistCommandline
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Bio.SeqIO.PhdIO
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DatabaseLoader
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EProtParsCommandline
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Bio.SeqIO.PirIO
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DatabaseLoader
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ESeqBootCommandline
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Bio.SeqIO.QualityIO
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DatabaseLoader
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ETandemCommandline
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Bio.SeqIO.SwissIO
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DatabaseLoader
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Est2GenomeCommandline
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Bio.SeqIO.TabIO
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DatabaseLoader
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FConsenseCommandline
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Bio.SeqIO
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DatabaseLoader
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FDNADistCommandline
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Bio.SeqIO._convert
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DatabaseLoader
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FDNAParsCommandline
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Bio.SeqIO._index
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DatabaseLoader
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FNeighborCommandline
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Bio.SeqRecord
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DatabaseLoader
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FProtDistCommandline
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Bio.SeqUtils.CheckSum
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Record
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FProtParsCommandline
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Bio.SeqUtils.CodonUsage
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HiddenMarkovModel
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FSeqBootCommandline
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Bio.SeqUtils.CodonUsageIndices
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Bio.MarkovModel
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FTreeDistCommandline
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Bio.SeqUtils.IsoelectricPoint
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Bio.MarkovModel
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FuzznucCommandline
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Bio.SeqUtils.MeltingTemp
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Bio.MarkovModel
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IepCommandline
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Bio.SeqUtils.ProtParam
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Bio.pairwise2
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NeedleCommandline
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Bio.SeqUtils.ProtParamData
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Bio.pairwise2
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PalindromeCommandline
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Bio.SeqUtils
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Bio.Align.Applications
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Primer3Commandline
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Bio.SeqUtils.lcc
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Bio.Data.IUPACData
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PrimerSearchCommandline
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Bio.Sequencing.Ace
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EventGenerator
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SeqretCommandline
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Bio.Sequencing.Applications._Novoalign
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Bio.PDB.FragmentMapper'
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TranalignCommandline
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Bio.Sequencing.Applications
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PrintFormat
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WaterCommandline
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Bio.Sequencing.Phd
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Bio.Sequencing
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Bio.Statistics
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Primers
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Bio.Statistics.lowess
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MMCIF2Dict
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Record
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Bio.SubsMat.FreqTable
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PrintFormat
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Amplifier
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Bio.SubsMat.MatrixInfo
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PrintFormat
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InputRecord
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Bio.SubsMat
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OutputRecord
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Bio.SwissProt.KeyWList
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DataHandler
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Bio.SwissProt.SProt
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Bio.Data.IUPACData
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StructureElement
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Bio.SwissProt
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Bio.pairwise2
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DataRecord
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Bio.Transcribe
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Bio.pairwise2
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EnzymeRecord
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Bio.Translate
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Bio.Nexus.Nexus
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Iterator
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Bio.UniGene
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Bio.Seq
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RecordParser
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Bio.WWW
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FragmentMapper
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_RecordConsumer
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Bio.Wise
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Bio.PDB.FragmentMapper'
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Record
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Bio.Wise.dnal
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Record
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Record
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Bio.Wise.psw
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Bio.MEME.Parser
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Reference
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Bio
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Bio.Motif.Parsers.MEME
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Record
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Bio.distance
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Bio.MEME.Parser
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ContentHandler
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Bio.kNN
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Bio.Motif.Parsers.MEME
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Parser
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Bio.listfns
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Nexus
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Record
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Bio.mathfns
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Reference
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FSSPAlignDict
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Bio.pairwise2
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Bio.MEME.Parser
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FSSPAlignRec
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Bio.stringfns
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Bio.Motif.Parsers.MEME
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FSSPHeader
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Bio.triefind
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Bio.MEME.Parser
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FSSPSumRec
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Bio.utils
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Bio.Motif.Parsers.MEME
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FSSPMultAlign
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BioSQL.BioSeq
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Bio.MarkovModel
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PosAlign
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BioSQL.BioSeqDatabase
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fff_rec
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BioSQL.DBUtils
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Ov3
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FastaAlignment
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BioSQL.Loader
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Ov5
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Iterator
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BioSQL
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Record
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Vector
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RecordParser
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SequenceParser
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SGMLHandle
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MutableSeq
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MyParser
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Seq
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SGMLStripper
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TwoCuts
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DBSeq
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Bio.Motif
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FilteredReader
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RestrictionBatch
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Instance
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SafeFitnessCrossover
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RestrictionType
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MEMEInstance
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GeneralPointCrossover
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Bio.ExPASy.Enzyme
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Bio.Align.Applications
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InterleaveCrossover
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Bio.ExPASy.Prodoc
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Record
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SinglePointCrossover
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Bio.ExPASy.Prosite
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Record
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TwoPointCrossover
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Bio.ExPASy.Prodoc
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UniformCrossover
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Bio.ExPASy.Prodoc
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Nexus
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GenerationEvolver
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Bio.ExPASy.Prodoc
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Bio.Parsers.spark
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SteadyStateEvolver
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Bio.ExPASy.Prodoc
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Bio.PDB.parse_pdb_header'
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SafeFitnessMutation
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Bio.ExPASy.Prodoc
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Record
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ConversionMutation
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Bio.SCOP
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SinglePositionMutation
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Alignment
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Bio.MarkovModel
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AlphabetEncoder
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Bio.Sequencing.Applications
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AbstractSelection
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AbstractCommandline
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DiversitySelection
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MEMEMotif
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Bio.Entrez
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TournamentSelection
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Bio.SCOP
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Connection
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Bio.SCOP
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Record
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Bio.Application
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FeatureQuery
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fff_rec
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ArgsParser
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TempFile
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Segment
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NdbParser
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FastaM10Iterator
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NCBIDictionary
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StockholmIterator
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Bio.PDB.Polypeptide
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Bio.MarkovModel
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AbstractDPAlgorithms
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MarkovModelBuilder
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Bio.Blast.NCBIStandalone
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TrainingSequence
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RestrictionType
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HotCache
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Record
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KDTree
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Bio.SwissProt
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Bio.UniGene
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Bio.PopGen.GenePop.Controller
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LogisticRegression
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Bio.SwissProt
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NCBIDictionary
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Bio.NMR.xpktools
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MEMEMotif
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Bio.SwissProt
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DisorderedEntityWrapper
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Bio.SwissProt
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MASTParser
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Vector
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_read_fragments()
(in
Bio.PDB.FragmentMapper'
)
__init__()
(in
MASTRecord
)
__setitem__()
(in
Dictionary
)
_read_ft()
(in
Bio.SwissProt
)
__init__()
(in
MEMEParser
)
__setitem__()
(in
MutableSeq
)
_read_headed_triangle_matrix()
(in
Bio.PopGen.GenePop.Controller
)
__init__()
(in
MEMERecord
)
__setitem__()
(in
_IndexedSeqFileDict
)
_read_id()
(in
Bio.SwissProt
)
__init__()
(in
_MASTConsumer
)
__setitem__()
(in
_RestrictedDict
)
_read_key_value()
(in
Bio.Geo
)
__init__()
(in
_MEMEConsumer
)
__setslice__()
(in
Chain
)
_read_oh()
(in
Bio.SwissProt
)
__init__()
(in
MarkovModel
)
__str__()
(in
PSSM
)
_read_ox()
(in
Bio.SwissProt
)
__init__()
(in
MaxEntropy
)
__str__()
(in
Alignment
)
_read_rc()
(in
Bio.SwissProt
)
__init__()
(in
Record
)
__str__()
(in
Motif
)
_read_rn()
(in
Bio.SwissProt
)
__init__()
(in
AlignAceCommandline
)
__str__()
(in
AbstractCommandline
)
_read_rx()
(in
Bio.SwissProt
)
__init__()
(in
CompareAceCommandline
)
__str__()
(in
_AbstractParameter
)
_read_table()
(in
Bio.PopGen.GenePop.Controller
)
__init__()
(in
AlignAceConsumer
)
__str__()
(in
_Argument
)
_read_triangle_matrix()
(in
Bio.PopGen.GenePop.Controller
)
__init__()
(in
AlignAceParser
)
__str__()
(in
_Option
)
_read_vertex_array()
(in
Bio.PDB.ResidueDepth'
)
__init__()
(in
CompareAceConsumer
)
__str__()
(in
_Switch
)
_readers
(in
Bio.Motif
)
__init__()
(in
CompareAceParser
)
__str__()
(in
Alignment
)
_readline_and_check_start()
(in
Bio.MarkovModel
)
__init__()
(in
MASTParser
)
__str__()
(in
Description
)
_record_key()
(in
_IndexedSeqFileDict
)
__init__()
(in
MASTRecord
)
__str__()
(in
HSP
)
_RecordConsumer
(in
Bio.Enzyme
)
__init__()
(in
MEMEInstance
)
__str__()
(in
ClustalAlignment
)
_RecordConsumer
__init__()
(in
MEMEMotif
)
__str__()
(in
MultipleAlignCL
)
_RecordConsumer
__init__()
(in
MEMEParser
)
__str__()
(in
Chain
)
_RecordConsumer
(in
Bio.PopGen.GenePop
)
__init__()
(in
MEMERecord
)
__str__()
(in
Crystal
)
_RecordConsumer
(in
Bio.Prosite.Prodoc
)
__init__()
(in
_MASTConsumer
)
__str__()
(in
Hetero
)
_RecordConsumer
(in
Bio.Prosite
)
__init__()
(in
_MEMEConsumer
)
__str__()
(in
CodonTable
)
_RecordConsumer
(in
Bio.SwissProt.SProt
)
__init__()
(in
ScoreDistribution
)
__str__()
(in
InputRecord
)
_RecordConsumer
(in
Bio.UniGene
)
__init__()
(in
Motif
)
__str__()
(in
DataRecord
)
_recover_alignments()
(in
Bio.pairwise2
)
__init__()
(in
Peaklist
)
__str__()
(in
EnzymeRecord
)
_reference_line()
(in
Reference
)
__init__()
(in
XpkEntry
)
__str__()
(in
Record
)
_remark_line()
(in
Reference
)
__init__()
(in
NaiveBayes
)
__str__()
(in
FastaAlignment
)
_remove_garbage()
(in
GenePopController
)
__init__()
(in
Record
)
__str__()
(in
Record
)
_remove_newlines()
(in
_BaseGenBankConsumer
)
__init__()
(in
ExtractUrls
)
__str__()
(in
Organism
)
_remove_spaces()
(in
_BaseGenBankConsumer
)
__init__()
(in
NetCatch
)
__str__()
(in
Feature
)
_replace_parenthesized_ambigs()
(in
Bio.Nexus.Nexus
)
__init__()
(in
Url
)
__str__()
(in
VerboseDict
)
_resolve()
(in
Nexus
)
__init__()
(in
AbstractLayer
)
__str__()
(in
VerboseList
)
_RestrictedDict
(in
Bio.SeqRecord
)
__init__()
(in
HiddenLayer
)
__str__()
(in
Location
)
_retrieve_annotations()
(in
BioSQL.BioSeq
)
__init__()
(in
InputLayer
)
__str__()
(in
Integer
)
_retrieve_comment()
(in
BioSQL.BioSeq
)
__init__()
(in
OutputLayer
)
__str__()
(in
Symbol
)
_retrieve_dbxrefs()
(in
BioSQL.BioSeq
)
__init__()
(in
BasicNetwork
)
__str__()
(in
Feature
)
_retrieve_features()
(in
BioSQL.BioSeq
)
__init__()
(in
MotifCoder
)
__str__()
(in
Record
)
_retrieve_location_qualifier_value()
(in
BioSQL.BioSeq
)
__init__()
(in
MotifFinder
)
__str__()
(in
Reference
)
_retrieve_qualifier_value()
(in
BioSQL.BioSeq
)
__init__()
(in
PatternIO
)
__str__()
(in
Record
)
_retrieve_reference()
(in
BioSQL.BioSeq
)
__init__()
(in
PatternRepository
)
__str__()
(in
Diagram
)
_retrieve_seq()
(in
BioSQL.BioSeq
)
__init__()
(in
DifferentialSchemaFitness
)
__str__()
(in
FeatureSet
)
_retrieve_taxon()
(in
BioSQL.BioSeq
)
__init__()
(in
GeneticAlgorithmFinder
)
__str__()
(in
GraphData
)
_rev_modify()
(in
NoCut
)
__init__()
(in
MostCountSchemaFitness
)
__str__()
(in
GraphSet
)
_rev_modify()
(in
OneCut
)
__init__()
(in
RandomMotifGenerator
)
__str__()
(in
Track
)
_rev_modify()
(in
TwoCuts
)
__init__()
(in
Schema
)
__str__()
(in
Record
)
_rms()
(in
SVDSuperimposer
)
__init__()
(in
SchemaCoder
)
__str__()
(in
Record
)
_rna_complement_table
(in
Bio.Seq
)
__init__()
(in
SchemaFactory
)
__str__()
(in
Record
)
_run_genepop()
(in
GenePopController
)
__init__()
(in
SchemaFinder
)
__str__()
(in
MarkovModel
)
_run_program()
(in
Local
)
__init__()
(in
SimpleFinisher
)
__str__()
(in
Motif
)
_safe_float()
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
SignatureCoder
)
__str__()
(in
Record
)
_safe_int()
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
SignatureFinder
)
__str__()
(in
ExtractUrls
)
_savedata()
(in
Record
)
__init__()
(in
ValidationIncreaseStop
)
__str__()
(in
NetCatch
)
_savekmeans()
(in
Record
)
__init__()
(in
ExampleManager
)
__str__()
(in
AbstractLayer
)
_savetree()
(in
Bio.Cluster
)
__init__()
(in
TrainingExample
)
__str__()
(in
Tree
)
_sbjct_re
(in
_HSPConsumer
)
__init__()
(in
Block
)
__str__()
(in
Interaction
)
_scan_3d()
(in
_Scanner
)
__init__()
(in
CharBuffer
)
__str__()
(in
Network
)
_scan_ac()
(in
_Scanner
)
__init__()
(in
Commandline
)
__str__()
(in
Reaction
)
_scan_ac()
(in
_Scanner
)
__init__()
(in
Nexus
)
__str__()
(in
Graph
)
_scan_accession()
(in
_Scanner
)
__init__()
(in
StepMatrix
)
__str__()
(in
HashSet
)
_scan_alignment()
(in
_Scanner
)
__init__()
(in
Chain
)
__str__()
(in
MultiGraph
)
_scan_alignment_header()
(in
_Scanner
)
__init__()
(in
Node
)
__str__()
(in
System
)
_scan_alignments()
(in
_Scanner
)
__init__()
(in
NodeData
)
__str__()
(in
Record
)
_scan_an()
(in
_Scanner
)
__init__()
(in
Tree
)
__str__()
(in
Record
)
_scan_annotated_matches()
(in
_MASTScanner
)
__init__()
(in
AbstractAtomPropertyMap
)
__str__()
(in
Prosite
)
_scan_annotated_matches()
(in
_MASTScanner
)
__init__()
(in
AbstractPropertyMap
)
__str__()
(in
PrositeMatch
)
_scan_ca()
(in
_Scanner
)
__init__()
(in
AbstractResiduePropertyMap
)
__str__()
(in
PrositeTerm
)
_scan_cc()
(in
_Scanner
)
__init__()
(in
Atom
)
__str__()
(in
PatternHit
)
_scan_cc()
(in
_Scanner
)
__init__()
(in
DisorderedAtom
)
__str__()
(in
RestrictionBatch
)
_scan_cc()
(in
_Scanner
)
__init__()
(in
Chain
)
__str__()
(in
RestrictionType
)
_scan_cf()
(in
_Scanner
)
__init__()
(in
DSSP
)
__str__()
(in
Record
)
_scan_copyright()
(in
_Scanner
)
__init__()
(in
ChainSelector
)
__str__()
(in
Record
)
_scan_copyrights()
(in
_Scanner
)
__init__()
(in
DisorderedEntityWrapper
)
__str__()
(in
Record
)
_scan_database_report()
(in
_Scanner
)
__init__()
(in
Entity
)
__str__()
(in
Domain
)
_scan_de()
(in
_Scanner
)
__init__()
(in
Fragment
)
__str__()
(in
Record
)
_scan_de()
(in
_Scanner
)
__init__()
(in
FragmentMapper
)
__str__()
(in
Node
)
_scan_de()
(in
_Scanner
)
__init__()
(in
ExposureCN
)
__str__()
(in
Residues
)
_scan_descriptions()
(in
_Scanner
)
__init__()
(in
HSExposureCA
)
__str__()
(in
MutableSeq
)
_scan_di()
(in
_Scanner
)
__init__()
(in
HSExposureCB
)
__str__()
(in
Seq
)
_scan_do()
(in
_Scanner
)
__init__()
(in
_AbstractHSExposure
)
__str__()
(in
UnknownSeq
)
_scan_dr()
(in
_Scanner
)
__init__()
(in
MMCIF2Dict
)
__str__()
(in
AfterPosition
)
_scan_dr()
(in
_Scanner
)
__init__()
(in
Model
)
__str__()
(in
BeforePosition
)
_scan_dr()
(in
_Scanner
)
__init__()
(in
NACCESS
)
__str__()
(in
BetweenPosition
)
_scan_dt()
(in
_Scanner
)
__init__()
(in
NACCESS_atomic
)
__str__()
(in
ExactPosition
)
_scan_dt()
(in
_Scanner
)
__init__()
(in
NeighborSearch
)
__str__()
(in
FeatureLocation
)
_scan_fns
(in
_Scanner
)
__init__()
(in
PDBIO
)
__str__()
(in
OneOfPosition
)
_scan_fns
(in
_Scanner
)
__init__()
(in
PDBList
)
__str__()
(in
PositionGap
)
_scan_fns
(in
_Scanner
)
__init__()
(in
PDBParser
)
__str__()
(in
Reference
)
_scan_ft()
(in
_Scanner
)
__init__()
(in
PSEA
)
__str__()
(in
SeqFeature
)
_scan_gn()
(in
_Scanner
)
__init__()
(in
CaPPBuilder
)
__str__()
(in
WithinPosition
)
_scan_header()
(in
_Scanner
)
__init__()
(in
PPBuilder
)
__str__()
(in
_IndexedSeqFileDict
)
_scan_header()
(in
_MASTScanner
)
__init__()
(in
_PPBuilder
)
__str__()
(in
SeqRecord
)
_scan_header()
(in
_MEMEScanner
)
__init__()
(in
DisorderedResidue
)
__str__()
(in
SeqMat
)
_scan_header()
(in
_MASTScanner
)
__init__()
(in
Residue
)
__str__()
(in
Translator
)
_scan_header()
(in
_MEMEScanner
)
__init__()
(in
ResidueDepth
)
__str__()
(in
Statistics
)
_scan_hsp()
(in
_Scanner
)
__init__()
(in
Structure
)
__str__()
(in
ColumnUnit
)
_scan_hsp_alignment()
(in
_Scanner
)
__init__()
(in
StructureAlignment
)
__str__()
(in
DBSeq
)
_scan_hsp_header()
(in
_Scanner
)
__init__()
(in
StructureBuilder
)
__sub__()
(in
Location
)
_scan_id()
(in
_Scanner
)
__init__()
(in
Superimposer
)
__sub__()
(in
Atom
)
_scan_id()
(in
_Scanner
)
__init__()
(in
Vector
)
__sub__()
(in
Fragment
)
_scan_id()
(in
_Scanner
)
__init__()
(in
EventGenerator
)
__sub__()
(in
Vector
)
_scan_kw()
(in
_Scanner
)
__init__()
(in
SGMLStrippingConsumer
)
__sub__()
(in
SeqMat
)
_scan_lengths()
(in
_Scanner
)
__init__()
(in
TaggingConsumer
)
__truediv__()
(in
RestrictionType
)
_scan_line()
(in
_Scanner
)
__init__()
(in
GenericASTBuilder
)
__version
(in
_InMemoryIndex
)
_scan_line()
(in
_Scanner
)
__init__()
(in
GenericASTMatcher
)
__version
(in
_ShelveIndex
)
_scan_line()
(in
_Scanner
)
__init__()
(in
GenericASTTraversal
)
__version_key
(in
_InMemoryIndex
)
_scan_ma()
(in
_Scanner
)
__init__()
(in
GenericParser
)
__version_key
(in
_ShelveIndex
)
_scan_masterslave_alignment()
(in
_Scanner
)
__init__()
(in
GenericScanner
)
__warningregistry__
(in
Bio.Align.FormatConvert
)
_scan_matches()
(in
_MASTScanner
)
__init__()
(in
Network
)
__warningregistry__
(in
Bio.AlignAce
)
_scan_matches()
(in
_MASTScanner
)
__init__()
(in
Reaction
)
__warningregistry__
(in
Bio.EZRetrieve
)
_scan_motifs()
(in
_MEMEScanner
)
__init__()
(in
Graph
)
__warningregistry__
(in
Bio.Fasta
)
_scan_motifs()
(in
_MEMEScanner
)
__init__()
(in
HashSet
)
__warningregistry__
(in
Bio.FilteredReader
)
_scan_names()
(in
_Scanner
)
__init__()
(in
MultiGraph
)
__warningregistry__
(in
Bio.MEME
)
_scan_nr()
(in
_Scanner
)
__init__()
(in
System
)
__warningregistry__
(in
Bio.Ndb
)
_scan_oc()
(in
_Scanner
)
__init__()
(in
Async
)
__warningregistry__
(in
Bio.NetCatch
)
_scan_og()
(in
_Scanner
)
__init__()
(in
DirectoryRetriever
)
__warningregistry__
(in
Bio.PubMed
)
_scan_oh()
(in
_Scanner
)
__init__()
(in
FileRetriever
)
__warningregistry__
(in
Bio.SCOP.FileIndex
)
_scan_one_pairwise_alignment()
(in
_Scanner
)
__init__()
(in
Local
)
__warningregistry__
(in
Bio.SwissProt.SProt
)
_scan_os()
(in
_Scanner
)
__init__()
(in
FDistAsync
)
__warningregistry__
(in
Bio.Transcribe
)
_scan_ox()
(in
_Scanner
)
__init__()
(in
SplitFDist
)
__warningregistry__
(in
Bio.Translate
)
_scan_pa()
(in
_Scanner
)
__init__()
(in
FDistController
)
__warningregistry__
(in
Bio.WWW
)
_scan_pairwise_alignments()
(in
_Scanner
)
__init__()
(in
Record
)
__warningregistry__
(in
Bio.distance
)
_scan_parameters()
(in
_Scanner
)
__init__()
(in
RecordParser
)
__warningregistry__
(in
Bio.mathfns
)
_scan_pe()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
__warningregistry__
(in
Bio.stringfns
)
_scan_pp()
(in
_Scanner
)
__init__()
(in
GenePopController
)
_AbstractDrawer
(in
Bio.Graphics.GenomeDiagram
)
_scan_pr()
(in
_Scanner
)
__init__()
(in
_FileIterator
)
_AbstractHSExposure
(in
Bio.PDB.HSExposure
)
_scan_pr()
(in
_Scanner
)
__init__()
(in
_GenePopCommandline
)
_AbstractParameter
(in
Bio.Application
)
_scan_profilewidth()
(in
_Scanner
)
__init__()
(in
EasyController
)
_accept()
(in
_PPBuilder
)
_scan_prosite_refs()
(in
_Scanner
)
__init__()
(in
Record
)
_accession_line()
(in
Record
)
_scan_ra()
(in
_Scanner
)
__init__()
(in
RecordParser
)
_add()
(in
ScoreDistribution
)
_scan_rc()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
_add_bioentry_dbxref()
(in
DatabaseLoader
)
_scan_record()
(in
_Scanner
)
__init__()
(in
SimCoalCache
)
_add_dbxref()
(in
DatabaseLoader
)
_scan_record()
(in
_Scanner
)
__init__()
(in
SimCoalCache
)
_add_diagram_for_sequence()
(in
MASTRecord
)
_scan_record()
(in
_Scanner
)
__init__()
(in
SimCoalController
)
_add_diagram_for_sequence()
(in
MASTRecord
)
_scan_record()
(in
_Scanner
)
__init__()
(in
PropertyManager
)
_add_diagram_from_buffer()
(in
_MASTConsumer
)
_scan_record()
(in
_Scanner
)
__init__()
(in
Dictionary
)
_add_diagram_from_buffer()
(in
_MASTConsumer
)
_scan_reference()
(in
_Scanner
)
__init__()
(in
Prosite
)
_add_feature()
(in
_FeatureConsumer
)
_scan_refs()
(in
_Scanner
)
__init__()
(in
PrositeMatch
)
_add_feature()
(in
_RecordConsumer
)
_scan_rl()
(in
_Scanner
)
__init__()
(in
PrositeTerm
)
_add_line_to_buffer()
(in
_MASTConsumer
)
_scan_rn()
(in
_Scanner
)
__init__()
(in
PatternHit
)
_add_line_to_buffer()
(in
_MASTConsumer
)
_scan_rounds()
(in
_Scanner
)
__init__()
(in
Dictionary
)
_add_match()
(in
MASTRecord
)
_scan_rp()
(in
_Scanner
)
__init__()
(in
Record
)
_add_match()
(in
MASTRecord
)
_scan_rt()
(in
_Scanner
)
__init__()
(in
RecordParser
)
_add_match_diagram()
(in
_MASTConsumer
)
_scan_ru()
(in
_Scanner
)
__init__()
(in
Reference
)
_add_match_diagram()
(in
_MASTConsumer
)
_scan_rx()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
_add_motif()
(in
MASTRecord
)
_scan_scores()
(in
_Scanner
)
__init__()
(in
Record
)
_add_motif()
(in
_MASTConsumer
)
_scan_sequence_data()
(in
_Scanner
)
__init__()
(in
RecordParser
)
_add_motif()
(in
MASTRecord
)
_scan_sq()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
_add_motif()
(in
_MASTConsumer
)
_scan_terminator()
(in
_Scanner
)
__init__()
(in
Dictionary
)
_add_motif()
(in
MotifFinder
)
_scan_terminator()
(in
_Scanner
)
__init__()
(in
PrintFormat
)
_add_motif_match()
(in
_MASTConsumer
)
_scan_terminator()
(in
_Scanner
)
__init__()
(in
Analysis
)
_add_motif_match()
(in
_MASTConsumer
)
_scan_text()
(in
_Scanner
)
__init__()
(in
FormattedSeq
)
_add_motif_with_info()
(in
_MEMEConsumer
)
_scan_threshold()
(in
_Scanner
)
__init__()
(in
RestrictionBatch
)
_add_motif_with_info()
(in
_MEMEConsumer
)
_Scanner
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
RestrictionType
)
_add_nodedata()
(in
Tree
)
_Scanner
(in
Bio.Compass
)
__init__()
(in
DictionaryBuilder
)
_add_numbering_table()
(in
FSSPAlign
)
_Scanner
(in
Bio.Enzyme
)
__init__()
(in
TypeCompiler
)
_add_qualifier()
(in
_FeatureConsumer
)
_Scanner
__init__()
(in
newenzyme
)
_add_seqfeature_dbxref()
(in
DatabaseLoader
)
_Scanner
(in
Bio.PopGen.GenePop
)
__init__()
(in
ConnectionError
)
_add_sequence()
(in
MASTRecord
)
_Scanner
(in
Bio.Prosite.Prodoc
)
__init__()
(in
FtpNameError
)
_add_sequence()
(in
MASTRecord
)
_Scanner
(in
Bio.Prosite
)
__init__()
(in
FtpPasswordError
)
_add_sequence_match_with_diagram()
(in
_MASTConsumer
)
_Scanner
(in
Bio.SwissProt.SProt
)
__init__()
(in
RebaseUpdate
)
_add_sequence_match_with_diagram()
(in
_MASTConsumer
)
_Scanner
(in
Bio.UniGene
)
__init__()
(in
Astral
)
_add_sig()
(in
SignatureFinder
)
_schema_from_motif()
(in
SchemaFactory
)
__init__()
(in
Index
)
_add_subtree()
(in
Tree
)
_score()
(in
Instance
)
__init__()
(in
Record
)
_adjust_charlabels()
(in
Nexus
)
_score()
(in
MEMEInstance
)
__init__()
(in
Record
)
_adjust_lines()
(in
Bio.Nexus.Nexus
)
_SCORE_GAP_EXTENSION
(in
Bio.Wise.dnal
)
__init__()
(in
Iterator
)
_alb_line2coords()
(in
Bio.Wise.dnal
)
_SCORE_GAP_START
(in
Bio.Wise.dnal
)
__init__()
(in
Record
)
_align()
(in
Bio.pairwise2
)
_SCORE_MATCH
(in
Bio.Wise.dnal
)
__init__()
(in
Domain
)
_AlignAce
(in
Bio.Motif.Applications
)
_SCORE_MISMATCH
(in
Bio.Wise.dnal
)
__init__()
(in
FileIndex
)
_AlignmentConsumer
(in
Bio.Blast.NCBIStandalone
)
_search()
(in
NonPalindromic
)
__init__()
(in
defaultdict
)
_all_blank()
(in
MarkovModelBuilder
)
_search()
(in
Palindromic
)
__init__()
(in
Record
)
_all_pseudo()
(in
MarkovModelBuilder
)
_secure_name()
(in
_XMLparser
)
__init__()
(in
Node
)
_allowed_lookups
(in
BioSQL.BioSeqDatabase
)
_security_check_parameters()
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
Res
)
_alphabet()
(in
Motif
)
_segment_line()
(in
Record
)
__init__()
(in
SeqMap
)
_alphabet()
(in
MASTRecord
)
_select_charged()
(in
IsoelectricPoint
)
__init__()
(in
SeqMapIndex
)
_alphabet()
(in
_MEMEConsumer
)
_SeqIO_to_alignment_iterator()
(in
Bio.AlignIO
)
__init__()
(in
Residues
)
_alphabet()
(in
MASTRecord
)
_SeqLength
(in
Bio.Search
)
__init__()
(in
Scop
)
_alphabet()
(in
_MEMEConsumer
)
_seqmatrix2strmatrix()
(in
Bio.Nexus.Nexus
)
__init__()
(in
SVDSuperimposer
)
_alphabet_from_input()
(in
FreqTable
)
_seqname()
(in
Instance
)
__init__()
(in
Algorithm
)
_alphabet_from_matrix()
(in
SeqMat
)
_seqname()
(in
MEMEInstance
)
__init__()
(in
Database
)
_any()
(in
Bio.Wise.dnal
)
_sequence()
(in
Instance
)
__init__()
(in
HSP
)
_apply_block_structure()
(in
Nexus
)
_sequence_line()
(in
Record
)
__init__()
(in
HSPSeq
)
_apply_clean_data()
(in
SGMLStrippingConsumer
)
_sequence_name()
(in
_MEMEConsumer
)
__init__()
(in
Hit
)
_argmaxes()
(in
Bio.MarkovModel
)
_sequence_name()
(in
_MEMEConsumer
)
__init__()
(in
HomologySeq
)
_Argument
(in
Bio.Application
)
_SequenceConsumer
(in
Bio.SwissProt.SProt
)
__init__()
(in
Query
)
_ATOM_FORMAT_STRING
(in
Bio.PDB.PDBIO'
)
_SequentialSeqFileDict
(in
Bio.SeqIO._index
)
__init__()
(in
Search
)
_atom_name_dict
(in
Bio.PDB.Residue
)
_set()
(in
Nexus
)
__init__()
(in
TableInfo
)
_authors_line()
(in
Reference
)
_set_centre()
(in
GraphData
)
__init__()
(in
_SeqLength
)
_back_translate_no_stop()
(in
Translator
)
_set_colors_and_shapes()
(in
ComparativeScatterPlot
)
__init__()
(in
MutableSeq
)
_backward()
(in
Bio.MarkovModel
)
_set_current_seq()
(in
_MASTConsumer
)
__init__()
(in
Seq
)
_backward_recursion()
(in
AbstractDPAlgorithms
)
_set_current_seq()
(in
_MASTConsumer
)
__init__()
(in
UnknownSeq
)
_backward_recursion()
(in
ScaledDPAlgorithms
)
_set_data()
(in
Seq
)
__init__()
(in
AbstractPosition
)
_base_count_line()
(in
Record
)
_set_function()
(in
_FeatureConsumer
)
__init__()
(in
AfterPosition
)
_BaseGenBankConsumer
_set_kind()
(in
AlignmentColumn
)
__init__()
(in
BeforePosition
)
_baum_welch()
(in
Bio.MarkovModel
)
_set_location()
(in
_FeatureConsumer
)
__init__()
(in
BetweenPosition
)
_baum_welch_one()
(in
Bio.MarkovModel
)
_set_location_info()
(in
_FeatureConsumer
)
__init__()
(in
ExactPosition
)
_blank_buffer()
(in
_MASTConsumer
)
_set_ordering_info()
(in
_FeatureConsumer
)
__init__()
(in
FeatureLocation
)
_blank_buffer()
(in
_MASTConsumer
)
_set_per_letter_annotations()
(in
SeqRecord
)
__init__()
(in
OneOfPosition
)
_BlastAllOrPgpCommandLine
(in
Bio.Blast.Applications
)
_set_seq()
(in
SeqRecord
)
__init__()
(in
PositionGap
)
_BlastCommandLine
(in
Bio.Blast.Applications
)
_set_up_genetic_algorithm()
(in
GeneticAlgorithmFinder
)
__init__()
(in
Reference
)
_BlastConsumer
(in
Bio.Blast.NCBIStandalone
)
_set_up_wheel()
(in
RouletteWheelSelection
)
__init__()
(in
SeqFeature
)
_BlastErrorConsumer
(in
Bio.Blast.NCBIStandalone
)
_set_xcentre()
(in
AbstractDrawer
)
__init__()
(in
WithinPosition
)
_bootstrap()
(in
Bio.Alphabet.IUPAC
)
_set_ycentre()
(in
AbstractDrawer
)
__init__()
(in
FastaWriter
)
_boundaries()
(in
Analysis
)
_ShelveIndex
(in
Bio.Index
)
__init__()
(in
InterlacedSequenceIterator
)
_build_align_cmdline()
(in
Bio.Wise
)
_ShelveIndex__version
(in
_ShelveIndex
)
__init__()
(in
SequenceIterator
)
_build_dnal_cmdline()
(in
Bio.Wise.dnal
)
_ShelveIndex__version_key
(in
_ShelveIndex
)
__init__()
(in
SequenceWriter
)
_build_exp_freq_mat()
(in
Bio.SubsMat
)
_shift()
(in
AbstractPosition
)
__init__()
(in
SequentialSequenceWriter
)
_build_log_odds_mat()
(in
Bio.SubsMat
)
_shift()
(in
FeatureLocation
)
__init__()
(in
PhdWriter
)
_build_obs_freq_mat()
(in
Bio.SubsMat
)
_shift()
(in
SeqFeature
)
__init__()
(in
QualPhredWriter
)
_build_path()
(in
NetCatch
)
_skip_file_header()
(in
FastaM10Iterator
)
__init__()
(in
AceDict
)
_build_structure()
(in
MMCIFParser
)
_skip_starstar()
(in
_Scanner
)
__init__()
(in
EmblDict
)
_build_subs_mat()
(in
Bio.SubsMat
)
_solexa_to_illumina_quality_str
(in
Bio.SeqIO.QualityIO
)
__init__()
(in
FastaDict
)
_cached_parser
(in
Bio.GenBank.LocationParser
)
_solexa_to_sanger_quality_str
(in
Bio.SeqIO.QualityIO
)
__init__()
(in
FastqIlluminaDict
)
_cached_scanner
(in
Bio.GenBank.LocationParser
)
_solexa_to_solexa_quality_str
(in
Bio.SeqIO.QualityIO
)
__init__()
(in
FastqSangerDict
)
_calc_diversities_fis()
(in
GenePopController
)
_sort()
(in
Chain
)
__init__()
(in
FastqSolexaDict
)
_calc_empirical_expects()
(in
Bio.MaxEntropy
)
_sort()
(in
Model
)
__init__()
(in
GenBankDict
)
_calc_f_sharp()
(in
Bio.MaxEntropy
)
_sort()
(in
Residue
)
__init__()
(in
IntelliGeneticsDict
)
_calc_ibd()
(in
GenePopController
)
_sort()
(in
Structure
)
__init__()
(in
PhdDict
)
_calc_model_expects()
(in
Bio.MaxEntropy
)
_sort_keys()
(in
Bio.NMR.xpktools
)
__init__()
(in
PirDict
)
_calc_p_class_given_x()
(in
Bio.MaxEntropy
)
_sort_keys_by_values()
(in
Bio.Nexus.Nexus
)
__init__()
(in
QualDict
)
_calculate_from_transitions()
(in
HiddenMarkovModel
)
_source_line()
(in
Record
)
__init__()
(in
SwissDict
)
_calculate_s_value()
(in
ScaledDPAlgorithms
)
_split_accessions()
(in
_BaseGenBankConsumer
)
__init__()
(in
TabDict
)
_changeset()
(in
Nexus
)
_split_keywords()
(in
_BaseGenBankConsumer
)
__init__()
(in
_FastqSeqFileDict
)
_chargeR()
(in
IsoelectricPoint
)
_split_reference_locations()
(in
_FeatureConsumer
)
__init__()
(in
_IndexedSeqFileDict
)
_charlabels()
(in
Nexus
)
_split_taxonomy()
(in
_BaseGenBankConsumer
)
__init__()
(in
_SequentialSeqFileDict
)
_charpartition()
(in
Nexus
)
_START
(in
GenericParser
)
__init__()
(in
SeqRecord
)
_charset()
(in
Nexus
)
_start()
(in
Instance
)
__init__()
(in
_RestrictedDict
)
_charstatelabels()
(in
Nexus
)
_start()
(in
MEMEInstance
)
__init__()
(in
CodonAdaptationIndex
)
_check_alphabet()
(in
Motif
)
_start_Hit()
(in
BlastParser
)
__init__()
(in
IsoelectricPoint
)
_check_alphabet()
(in
Motif
)
_start_Hsp()
(in
BlastParser
)
__init__()
(in
MissingTable
)
_check_is_public()
(in
Bio.DocSQL
)
_start_Iteration()
(in
BlastParser
)
__init__()
(in
ProteinAnalysis
)
_check_length()
(in
Motif
)
_statelabels()
(in
Nexus
)
__init__()
(in
ACEFileRecord
)
_check_length()
(in
Motif
)
_stateset()
(in
Nexus
)
__init__()
(in
Contig
)
_check_taxlabels()
(in
Nexus
)
_str_line()
(in
Alignment
)
__init__()
(in
Reads
)
_check_type_compatible()
(in
Bio.Alphabet
)
_strand()
(in
Instance
)
__init__()
(in
af
)
_check_value()
(in
AbstractCommandline
)
_strand()
(in
MEMEInstance
)
__init__()
(in
bs
)
_CHOMP
(in
Bio.SwissProt.SProt
)
_structures()
(in
Record
)
__init__()
(in
ct
)
_chomp()
(in
_RecordConsumer
)
_structures()
(in
Record
)
__init__()
(in
ds
)
_chop_end_codes()
(in
Bio.PDB.parse_pdb_header'
)
_sub_set()
(in
Analysis
)
__init__()
(in
qa
)
_chop_end_misc()
(in
Bio.PDB.parse_pdb_header'
)
_substrate()
(in
Record
)
__init__()
(in
rd
)
_ChromosomeComponent
(in
Bio.Graphics.BasicChromosome
)
_Switch
(in
Bio.Application
)
__init__()
(in
rt
)
_CircularDrawer
(in
Bio.Graphics.GenomeDiagram
)
_sysname()
(in
Record
)
__init__()
(in
wa
)
_classify_alphabet_for_nexus()
(in
NexusWriter
)
_table_h
(in
Bio.SeqUtils.CheckSum
)
__init__()
(in
wr
)
_classname()
(in
Record
)
_taxlabels()
(in
Nexus
)
__init__()
(in
NovoalignCommandline
)
_clean()
(in
_RecordConsumer
)
_taxpartition()
(in
Nexus
)
__init__()
(in
Record
)
_clean_alignments()
(in
Bio.pairwise2
)
_taxset()
(in
Nexus
)
__init__()
(in
FreqTable
)
_clean_data()
(in
_RecordConsumer
)
_TCoffee
(in
Bio.Align.Applications
)
__init__()
(in
SeqMat
)
_clean_location()
(in
_BaseGenBankConsumer
)
_test()
(in
Bio.Align.Generic
)
__init__()
(in
Record
)
_clean_record()
(in
_RecordConsumer
)
_test()
(in
Bio.AlignIO.StockholmIO
)
__init__()
(in
Record
)
_clean_references()
(in
_RecordConsumer
)
_test()
(in
Bio.AlignIO
)
__init__()
(in
Reference
)
_clean_translation()
(in
FeatureValueCleaner
)
_test()
(in
Bio.Application
)
__init__()
(in
Dictionary
)
_clear()
(in
SVDSuperimposer
)
_test()
(in
Bio.Clustalw
)
__init__()
(in
Record
)
_clear_parameter()
(in
AbstractCommandline
)
_test()
(in
Bio.DocSQL
)
__init__()
(in
RecordParser
)
_Clustalw
(in
Bio.Align.Applications
)
_test()
(in
Bio.GFF
)
__init__()
(in
Reference
)
_CMDLINE_DNAL
(in
Bio.Wise.dnal
)
_test()
(in
Bio.KEGG.Compound
)
__init__()
(in
SequenceParser
)
_CMDLINE_FGREP_COUNT
(in
Bio.Wise.dnal
)
_test()
(in
Bio.KEGG.Enzyme
)
__init__()
(in
_RecordConsumer
)
_CMDLINE_PSW
(in
Bio.Wise.psw
)
_test()
(in
Bio.Motif
)
__init__()
(in
_SequenceConsumer
)
_codeset()
(in
Nexus
)
_test()
(in
Bio.Seq
)
__init__()
(in
Transcribe
)
_codonposset()
(in
Nexus
)
_test()
(in
Bio.SeqIO.AceIO
)
__init__()
(in
Translator
)
_cofactor()
(in
Record
)
_test()
(in
Bio.SeqIO.PhdIO
)
__init__()
(in
Iterator
)
_col_ave()
(in
Bio.NMR.NOEtools
)
_test()
(in
Bio.SeqIO.QualityIO
)
__init__()
(in
ProtsimLine
)
_collapse_buffer()
(in
_MASTConsumer
)
_test()
(in
Bio.SeqIO
)
__init__()
(in
Record
)
_collapse_buffer()
(in
_MASTConsumer
)
_test()
(in
Bio.SeqRecord
)
__init__()
(in
RecordParser
)
_color_from_count()
(in
ChromosomeCounts
)
_test()
(in
Bio.Statistics.lowess
)
__init__()
(in
STSLine
)
_Colors
(in
Bio.Graphics.GenomeDiagram
)
_test()
(in
Bio.Wise
)
__init__()
(in
SequenceLine
)
_commandline()
(in
_MEMEConsumer
)
_test()
(in
Bio.Wise.dnal
)
__init__()
(in
UnigeneProtsimRecord
)
_commandline()
(in
_MEMEConsumer
)
_test()
(in
Bio.Wise.psw
)
__init__()
(in
UnigeneRecord
)
_comment()
(in
Record
)
_test_dist()
(in
PPBuilder
)
__init__()
(in
UnigeneSTSRecord
)
_comment_line()
(in
Record
)
_test_equivalence()
(in
StructureAlignment
)
__init__()
(in
UnigeneSequenceRecord
)
_compact4nexus()
(in
Bio.Nexus.Nexus
)
_test_global_hz_both()
(in
GenePopController
)
__init__()
(in
_RecordConsumer
)
_consensus()
(in
Motif
)
_test_normal()
(in
Analysis
)
__init__()
(in
RequestLimiter
)
_consensus_alphabet()
(in
Bio.Alphabet
)
_test_pop_hz_both()
(in
GenePopController
)
__init__()
(in
Statistics
)
_consensus_base_alphabet()
(in
Bio.Alphabet
)
_test_reverse()
(in
Analysis
)
__init__()
(in
AlignmentColumn
)
_consrtm_line()
(in
Reference
)
_title()
(in
Nexus
)
__init__()
(in
ColumnUnit
)
_consume_entry()
(in
BlastTableReader
)
_title_line()
(in
Reference
)
__init__()
(in
kNN
)
_consume_header()
(in
BlastTableReader
)
_to_fasta()
(in
Motif
)
__init__()
(in
affine_penalty
)
_Consumer
(in
Bio.Compass
)
_to_horizontal_matrix()
(in
Motif
)
__init__()
(in
dictionary_match
)
_contents()
(in
Bio.NaiveBayes
)
_to_jaspar_pfm()
(in
Motif
)
__init__()
(in
identity_match
)
_contig_line()
(in
Record
)
_to_transfac()
(in
Motif
)
__init__()
(in
DBSeq
)
_convert
(in
Bio.SeqIO
)
_to_vertical_matrix()
(in
Motif
)
__init__()
(in
DBSeqRecord
)
_convert_to_python_numbers()
(in
_BaseGenBankConsumer
)
_toobj()
(in
_InMemoryIndex
)
__init__()
(in
Adaptor
)
_converter
(in
Bio.SeqIO._convert
)
_tostr()
(in
_InMemoryIndex
)
__init__()
(in
BioSeqDatabase
)
_copy_and_check()
(in
Bio.MarkovModel
)
_Track
(in
Bio.Graphics.GenomeDiagram
)
__init__()
(in
DBServer
)
_corr()
(in
Bio.MEME.Motif
)
_train_iis()
(in
Bio.MaxEntropy
)
__init__()
(in
Generic_dbutils
)
_correct_matrix()
(in
SeqMat
)
_translate()
(in
Nexus
)
__init__()
(in
DatabaseLoader
)
_count_codons()
(in
CodonAdaptationIndex
)
_translate_id()
(in
AbstractAtomPropertyMap
)
__init__()
(in
DatabaseRemover
)
_count_emissions()
(in
KnownStateTrainer
)
_translate_id()
(in
AbstractPropertyMap
)
__iter__()
(in
Alignment
)
_count_transitions()
(in
KnownStateTrainer
)
_translate_id()
(in
AbstractResiduePropertyMap
)
__iter__()
(in
AlignmentIterator
)
_crossover()
(in
GeneralPointCrossover
)
_translate_id()
(in
Chain
)
__iter__()
(in
Iterator
)
_crossover()
(in
InterleaveCrossover
)
_translate_str()
(in
Bio.Seq
)
__iter__()
(in
Query
)
_crossover()
(in
TwoCrossover
)
_tree()
(in
Nexus
)
__iter__()
(in
Iterator
)
_data_map()
(in
Bio.NMR.NOEtools
)
_treepartition()
(in
Nexus
)
__iter__()
(in
Iterator
)
_database()
(in
MASTRecord
)
_treeset()
(in
Nexus
)
__iter__()
(in
UndoHandle
)
_database()
(in
_MASTConsumer
)
_treesort()
(in
Bio.Cluster
)
__iter__()
(in
Iterator
)
_database()
(in
MASTRecord
)
_try_open_read()
(in
Bio.NMR.xpktools
)
__iter__()
(in
AbstractPropertyMap
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(in
_MASTConsumer
)
_try_open_write()
(in
Bio.NMR.xpktools
)
__iter__()
(in
Entity
)
_DatabaseReportConsumer
(in
Bio.Blast.NCBIStandalone
)
_unhandled()
(in
AbstractConsumer
)
__iter__()
(in
_FileIterator
)
_datafile()
(in
_MEMEConsumer
)
_unhandled_section()
(in
AbstractConsumer
)
__iter__()
(in
InterlacedSequenceIterator
)
_datafile()
(in
_MEMEConsumer
)
_uniform_norm()
(in
Bio.MarkovModel
)
__iter__()
(in
SequenceIterator
)
_db_source_line()
(in
Record
)
_unique_label()
(in
Bio.Nexus.Nexus
)
__iter__()
(in
SeqRecord
)
_dblink_line()
(in
Record
)
_unknown_nexus_block()
(in
Nexus
)
__iter__()
(in
Iterator
)
_dblinks()
(in
Record
)
_Update
(in
Bio.Restriction
)
__le__()
(in
RestrictionType
)
_dblinks()
(in
Record
)
_utree()
(in
Nexus
)
__len__()
(in
Alignment
)
_dbutils
(in
BioSQL.DBUtils
)
_validate()
(in
AbstractCommandline
)
__len__()
(in
Chain
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_default_wrap()
(in
Bio.KEGG
)
_validate()
(in
SeqretCommandline
)
__len__()
(in
Crystal
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_definition_line()
(in
Record
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_validate()
(in
_EmbossCommandLine
)
__len__()
(in
Hetero
)
_DescriptionConsumer
(in
Bio.Blast.NCBIStandalone
)
_verify_test()
(in
Bio.Prosite.Pattern
)
__len__()
(in
fff_rec
)
_determine_position()
(in
BarChartDistribution
)
_version()
(in
MASTRecord
)
__len__()
(in
NCBIDictionary
)
_diagnose_error()
(in
BlastErrorParser
)
_version()
(in
_MASTConsumer
)
__len__()
(in
AbstractDrawer
)
_diagnostics
(in
RetrieveSeqname
)
_version()
(in
_MEMEConsumer
)
__len__()
(in
FeatureSet
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(in
Bio.Graphics.GenomeDiagram
)
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(in
MASTRecord
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(in
GraphData
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(in
Bio.Align.Applications
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(in
_MASTConsumer
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(in
GraphSet
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(in
CAPSMap
)
_version()
(in
_MEMEConsumer
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__len__()
(in
Motif
)
_digest_with()
(in
CAPSMap
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(in
Record
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__len__()
(in
AbstractPropertyMap
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(in
Nexus
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(in
Bio.MarkovModel
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__len__()
(in
Entity
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(in
Record
)
_walk()
(in
Tree
)
__len__()
(in
Fragment
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(in
Bio.Seq
)
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(in
ProteinAnalysis
)
__len__()
(in
HashSet
)
_domain_re
(in
Bio.SCOP
)
_wgs_line()
(in
Record
)
__len__()
(in
Dictionary
)
_draw_arc()
(in
CircularDrawer
)
_wgs_scafld_line()
(in
Record
)
__len__()
(in
Prosite
)
_draw_arc_arrow()
(in
CircularDrawer
)
_wrap_kegg()
(in
Bio.KEGG
)
__len__()
(in
PrositeMatch
)
_draw_distributions()
(in
DistributionPage
)
_wrap_location()
(in
GenBankWriter
)
__len__()
(in
Dictionary
)
_draw_label()
(in
Chromosome
)
_wrapped_genbank()
(in
Bio.GenBank.Record
)
__len__()
(in
Dictionary
)
_draw_label()
(in
ChromosomeSegment
)
_write()
(in
Bio.Graphics
)
__len__()
(in
FormattedSeq
)
_draw_legend()
(in
Organism
)
_write()
(in
Motif
)
__len__()
(in
RestrictionType
)
_draw_legend()
(in
DistributionPage
)
_write_feature()
(in
GenBankWriter
)
__len__()
(in
Hit
)
_draw_scatter_plot()
(in
ComparativeScatterPlot
)
_write_feature_qualifier()
(in
GenBankWriter
)
__len__()
(in
_SeqLength
)
_draw_segment()
(in
ChromosomeSegment
)
_write_kegg()
(in
Bio.KEGG
)
__len__()
(in
MutableSeq
)
_draw_segment()
(in
TelomereSegment
)
_write_multi_entries()
(in
GenBankWriter
)
__len__()
(in
Seq
)
_draw_subcomponents()
(in
ChromosomeSegment
)
_write_multi_line()
(in
GenBankWriter
)
__len__()
(in
UnknownSeq
)
_draw_title()
(in
Organism
)
_write_record()
(in
StockholmWriter
)
__len__()
(in
InterlacedSequenceIterator
)
_draw_title()
(in
ComparativeScatterPlot
)
_write_sequence()
(in
GenBankWriter
)
__len__()
(in
SeqRecord
)
_draw_title()
(in
BarChartDistribution
)
_write_single_line()
(in
GenBankWriter
)
__len__()
(in
Dictionary
)
_draw_title()
(in
DistributionPage
)
_write_the_first_line()
(in
GenBankWriter
)
__len__()
(in
DBSeq
)
_drop()
(in
Ambiguous
)
_XMLparser
(in
Bio.Blast.NCBIXML
)
__lt__()
(in
RestrictionType
)
_drop()
(in
Defined
)
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