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biopython
v1.71.0
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Bio.Affy.CelFile
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Summary
Functions
read/0
read_v3/0
read_v4/0
Bio.Affy.CelFile.ParserError
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Summary
Functions
__init__/0
Bio.Affy.CelFile.Record
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Summary
Functions
__init__/0
Bio.Align.AlignInfo
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Summary
Functions
print_info_content/0
Bio.Align.AlignInfo.PSSM
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Summary
Functions
__init__/0
get_residue/0
Bio.Align.AlignInfo.SummaryInfo
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Summary
Functions
__init__/0
_get_all_letters/0
_get_base_letters/0
_get_base_replacements/0
_get_column_info_content/0
_get_gap_char/0
_get_letter_freqs/0
_guess_consensus_alphabet/0
_pair_replacement/0
dumb_consensus/0
gap_consensus/0
information_content/0
pos_specific_score_matrix/0
replacement_dictionary/0
Bio.AlignIO.ClustalIO
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Bio.AlignIO.ClustalIO.ClustalIterator
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Bio.AlignIO.ClustalIO.ClustalWriter
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Summary
Functions
write_alignment/0
Bio.AlignIO.EmbossIO
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Bio.AlignIO.EmbossIO.EmbossIterator
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Bio.AlignIO.EmbossIO.EmbossWriter
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Summary
Functions
write_alignment/0
Bio.AlignIO.FastaIO
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Summary
Functions
FastaM10Iterator/0
_extract_alignment_region/0
build_hsp/0
Bio.AlignIO.Interfaces
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Bio.AlignIO.Interfaces.AlignmentIterator
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Summary
Functions
__init__/0
__iter__/0
__next__/0
next/0
Bio.AlignIO.Interfaces.AlignmentWriter
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Summary
Functions
__init__/0
clean/0
write_file/0
Bio.AlignIO.Interfaces.SequentialAlignmentWriter
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Summary
Functions
__init__/0
write_alignment/0
write_file/0
write_footer/0
write_header/0
Bio.AlignIO.MafIO
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Summary
Functions
MafIterator/0
Bio.AlignIO.MafIO.MafIndex
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Summary
Functions
__check_existing_db/0
__init__/0
__len__/0
__maf_indexer/0
__make_new_index/0
_get_record/0
_region2bin/0
_ucscbin/0
get_spliced/0
search/0
Bio.AlignIO.MafIO.MafWriter
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Summary
Functions
_write_record/0
write_alignment/0
write_header/0
Bio.AlignIO.MauveIO
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Summary
Functions
_identifier_split/0
Bio.AlignIO.MauveIO.MauveIterator
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Summary
Functions
__next__/0
Bio.AlignIO.MauveIO.MauveWriter
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Summary
Functions
__init__/0
_write_record/0
write_alignment/0
Bio.AlignIO.NexusIO
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Summary
Functions
NexusIterator/0
Bio.AlignIO.NexusIO.NexusWriter
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Summary
Functions
_classify_alphabet_for_nexus/0
write_file/0
Bio.AlignIO.PhylipIO
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Bio.AlignIO.PhylipIO.PhylipIterator
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Summary
Functions
__next__/0
_split_id/0
Bio.AlignIO.PhylipIO.RelaxedPhylipIterator
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Summary
Functions
_split_id/0
Bio.AlignIO.PhylipIO.RelaxedPhylipWriter
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Summary
Functions
write_alignment/0
Bio.AlignIO.PhylipIO.SequentialPhylipIterator
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Bio.AlignIO.PhylipIO.SequentialPhylipWriter
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Summary
Functions
write_alignment/0
Bio.AlignIO.StockholmIO
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Bio.AlignIO.StockholmIO.StockholmIterator
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Summary
Functions
__next__/0
_get_meta_data/0
_identifier_split/0
_populate_meta_data/0
Bio.AlignIO.StockholmIO.StockholmWriter
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Summary
Functions
_write_record/0
write_alignment/0
Bio.Alphabet.IUPAC
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Bio.Alphabet.IUPAC.ExtendedIUPACDNA
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Bio.Alphabet.IUPAC.ExtendedIUPACProtein
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Bio.Alphabet.IUPAC.IUPACAmbiguousDNA
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Bio.Alphabet.IUPAC.IUPACAmbiguousRNA
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Bio.Alphabet.IUPAC.IUPACProtein
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Bio.Alphabet.IUPAC.IUPACUnambiguousDNA
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Bio.Alphabet.IUPAC.IUPACUnambiguousRNA
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Bio.Alphabet.Reduced
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Bio.Alphabet.Reduced.HPModel
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Bio.Alphabet.Reduced.Murphy10
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Bio.Alphabet.Reduced.Murphy15
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Bio.Alphabet.Reduced.Murphy4
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Bio.Alphabet.Reduced.Murphy8
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Bio.Alphabet.Reduced.PC5
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Bio.Blast.Applications
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Summary
Functions
_test/0
Bio.Blast.Applications.NcbiblastformatterCommandline
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Summary
Functions
__init__/0
Bio.Blast.NCBIStandalone
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Bio.Blast.NCBIStandalone.BlastErrorParser
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Summary
Functions
__init__/0
_diagnose_error/0
parse/0
Bio.Blast.NCBIStandalone.BlastParser
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Summary
Functions
__init__/0
parse/0
Bio.Blast.NCBIStandalone.Iterator
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Summary
Functions
__init__/0
__next__/0
next/0
Bio.Blast.NCBIStandalone.LowQualityBlastError
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Bio.Blast.NCBIStandalone.PSIBlastParser
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Summary
Functions
__init__/0
parse/0
Bio.Blast.NCBIStandalone.ShortQueryBlastError
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Bio.Blast.NCBIWWW
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Summary
Functions
_parse_qblast_ref_page/0
qblast/0
Bio.Blast.NCBIXML
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Summary
Functions
parse/0
read/0
Bio.Blast.NCBIXML.BlastParser
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Summary
Functions
__init__/0
_end_BlastOutput_db/0
_end_BlastOutput_hits/0
_end_BlastOutput_program/0
_end_BlastOutput_query_ID/0
_end_BlastOutput_query_def/0
_end_BlastOutput_query_len/0
_end_BlastOutput_reference/0
_end_BlastOutput_version/0
_end_Hit_accession/0
_end_Hit_def/0
_end_Hit_id/0
_end_Hsp_align_len/0
_end_Hsp_bit_score/0
_end_Hsp_evalue/0
_end_Hsp_gaps/0
_end_Hsp_hit_frame/0
_end_Hsp_hit_from/0
_end_Hsp_hit_to/0
_end_Hsp_hseq/0
_end_Hsp_identity/0
_end_Hsp_midline/0
_end_Hsp_positive/0
_end_Hsp_qseq/0
_end_Hsp_query_frame/0
_end_Hsp_query_from/0
_end_Hsp_query_to/0
_end_Hsp_score/0
_end_Iteration_query_ID/0
_end_Iteration_query_def/0
_end_Iteration_query_len/0
_end_Parameters_expect/0
_end_Parameters_filter/0
_end_Parameters_gap_extend/0
_end_Parameters_gap_open/0
_end_Parameters_matrix/0
_end_Parameters_sc_match/0
_end_Parameters_sc_mismatch/0
_end_Statistics_db_len/0
_end_Statistics_db_num/0
_end_Statistics_eff_space/0
_end_Statistics_entropy/0
_end_Statistics_hsp_len/0
_end_Statistics_kappa/0
_end_Statistics_lambda/0
reset/0
Bio.Blast.ParseBlastTable
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Bio.Blast.ParseBlastTable.BlastTableEntry
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Summary
Functions
__init__/0
Bio.Blast.ParseBlastTable.BlastTableReader
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Summary
Functions
__init__/0
next/0
Bio.Blast.ParseBlastTable.BlastTableRec
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Summary
Functions
__init__/0
Bio.Blast.Record
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Bio.Blast.Record.Alignment
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Summary
Functions
__init__/0
Bio.Blast.Record.Blast
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Summary
Functions
__init__/0
Bio.Blast.Record.DatabaseReport
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Summary
Functions
__init__/0
Bio.Blast.Record.Description
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Summary
Functions
__init__/0
Bio.Blast.Record.HSP
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Summary
Functions
__init__/0
Bio.Blast.Record.Header
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Summary
Functions
__init__/0
Bio.Blast.Record.MultipleAlignment
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Summary
Functions
__init__/0
to_generic/0
Bio.Blast.Record.PSIBlast
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Summary
Functions
__init__/0
Bio.Blast.Record.Parameters
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Summary
Functions
__init__/0
Bio.Blast.Record.Round
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Summary
Functions
__init__/0
Bio.Data.CodonTable
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Summary
Functions
list_ambiguous_codons/0
make_back_table/0
register_ncbi_table/0
Bio.Data.CodonTable.AmbiguousCodonTable
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Summary
Functions
__init__/0
Bio.Data.CodonTable.AmbiguousForwardTable
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Summary
Functions
__init__/0
Bio.Data.CodonTable.CodonTable
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Summary
Functions
__init__/0
__str__/0
Bio.Data.CodonTable.NCBICodonTable
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Summary
Functions
__init__/0
Bio.Data.CodonTable.NCBICodonTableDNA
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Bio.Data.CodonTable.NCBICodonTableRNA
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Bio.Data.CodonTable.TranslationError
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Bio.Data.IUPACData
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Bio.Data.SCOPData
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Bio.DocSQL
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Bio.DocSQL.Create
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Summary
Functions
__init__/0
Bio.DocSQL.Insert
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Summary
Functions
__init__/0
Bio.DocSQL.IterationCursor
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Summary
Functions
__init__/0
next/0
Bio.DocSQL.NoInsertionError
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Bio.DocSQL.Query
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Summary
Functions
__init__/0
Bio.DocSQL.QueryAll
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Summary
Functions
__init__/0
Bio.DocSQL.QueryAllFirstItem
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Bio.DocSQL.QueryGeneric
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Summary
Functions
__init__/0
Bio.DocSQL.QueryRow
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Summary
Functions
__init__/0
Bio.DocSQL.QuerySingle
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Summary
Functions
__init__/0
Bio.DocSQL.Update
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Bio.Emboss.Applications
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Bio.Emboss.Applications.DiffseqCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.EInvertedCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.ETandemCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.Est2GenomeCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FConsenseCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FDNADistCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FDNAParsCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FNeighborCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FProtDistCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FProtParsCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FSeqBootCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FTreeDistCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.FuzznucCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.NeedleCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.NeedleallCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.PalindromeCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.PrimerSearchCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.SeqmatchallCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.SeqretCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.StretcherCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.TranalignCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Applications.WaterCommandline
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Summary
Functions
__init__/0
Bio.Emboss.Primer3
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Summary
Functions
parse/0
read/0
Bio.Emboss.Primer3.Primers
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Summary
Functions
__init__/0
__len__/0
Bio.Emboss.Primer3.Record
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Summary
Functions
__init__/0
Bio.Emboss.PrimerSearch
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Summary
Functions
read/0
Bio.Emboss.PrimerSearch.Amplifier
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Summary
Functions
__init__/0
Bio.Emboss.PrimerSearch.InputRecord
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Summary
Functions
__init__/0
add_primer_set/0
Bio.Emboss.PrimerSearch.OutputRecord
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Summary
Functions
__init__/0
Bio.Entrez.Parser
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Bio.Entrez.Parser.CorruptedXMLError
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Summary
Functions
__init__/0
Bio.Entrez.Parser.DataHandler
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Summary
Functions
__init__/0
elementDecl/0
externalEntityRefHandler/0
read/0
Bio.Entrez.Parser.DictionaryElement
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Bio.Entrez.Parser.IntegerElement
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Bio.Entrez.Parser.ListElement
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Bio.Entrez.Parser.NotXMLError
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Summary
Functions
__init__/0
Bio.Entrez.Parser.StringElement
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Bio.Entrez.Parser.StructureElement
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Summary
Functions
__init__/0
Bio.Entrez.Parser.UnicodeElement
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Bio.Entrez.Parser.ValidationError
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Summary
Functions
__init__/0
Bio.ExPASy.Enzyme
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Summary
Functions
parse/0
read/0
Bio.ExPASy.Enzyme.Record
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Summary
Functions
__init__/0
Bio.ExPASy.Prodoc
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Summary
Functions
parse/0
read/0
Bio.ExPASy.Prodoc.Record
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Summary
Functions
__init__/0
Bio.ExPASy.Prodoc.Reference
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Summary
Functions
__init__/0
Bio.ExPASy.Prosite
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Summary
Functions
parse/0
read/0
Bio.ExPASy.Prosite.Record
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Summary
Functions
__init__/0
Bio.ExPASy.ScanProsite
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Summary
Functions
read/0
scan/0
Bio.ExPASy.ScanProsite.ContentHandler
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Summary
Functions
__init__/0
Bio.ExPASy.ScanProsite.Parser
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Summary
Functions
__init__/0
Bio.ExPASy.ScanProsite.Record
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Summary
Functions
__init__/0
Bio.FSSP.FSSPTools
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Summary
Functions
filter/0
mult_align/0
name_filter/0
Bio.FSSP.FSSPTools.FSSPAlign
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Bio.FSSP.FSSPTools.FSSPMultAlign
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Summary
Functions
__init__/0
Bio.File.UndoHandle
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Summary
Functions
__enter__/0
__exit__/0
__getattr__/0
__init__/0
__iter__/0
__next__/0
next/0
peekline/0
read/0
readline/0
readlines/0
saveline/0
seek/0
tell/0
Bio.GA.Crossover.General
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Bio.GA.Crossover.General.SafeFitnessCrossover
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Summary
Functions
__init__/0
do_crossover/0
Bio.GA.Crossover.GeneralPoint
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Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
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Summary
Functions
__init__/0
_crossover/0
_generate_locs/0
do_crossover/0
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover
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Summary
Functions
__init__/0
Bio.GA.Crossover.GeneralPoint.TwoCrossover
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Summary
Functions
_crossover/0
_generate_locs/0
Bio.GA.Crossover.Point
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Bio.GA.Crossover.Point.SinglePointCrossover
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Summary
Functions
__init__/0
Bio.GA.Crossover.TwoPoint
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Bio.GA.Crossover.TwoPoint.TwoPointCrossover
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Summary
Functions
__init__/0
Bio.GA.Crossover.Uniform
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Bio.GA.Crossover.Uniform.UniformCrossover
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Summary
Functions
__init__/0
do_crossover/0
Bio.GA.Evolver
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Bio.GA.Evolver.GenerationEvolver
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Summary
Functions
__init__/0
evolve/0
Bio.GA.Evolver.SteadyStateEvolver
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Summary
Functions
__init__/0
Bio.GA.Mutation.General
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Bio.GA.Mutation.General.SafeFitnessMutation
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Summary
Functions
__init__/0
mutate/0
Bio.GA.Mutation.Simple
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Bio.GA.Mutation.Simple.ConversionMutation
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Summary
Functions
__init__/0
mutate/0
Bio.GA.Mutation.Simple.SinglePositionMutation
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Summary
Functions
__init__/0
mutate/0
Bio.GA.Organism
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Summary
Functions
function_population/0
random_population/0
Bio.GA.Organism.Organism
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Summary
Functions
__eq__/0
__ge__/0
__gt__/0
__init__/0
__le__/0
__lt__/0
__ne__/0
__str__/0
copy/0
recalculate_fitness/0
Bio.GA.Repair.Stabilizing
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Bio.GA.Repair.Stabilizing.AmbiguousRepair
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Summary
Functions
__init__/0
repair/0
Bio.GA.Selection.Abstract
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Bio.GA.Selection.Abstract.AbstractSelection
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Summary
Functions
__init__/0
mutate_and_crossover/0
Bio.GA.Selection.Diversity
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Bio.GA.Selection.Diversity.DiversitySelection
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Summary
Functions
__init__/0
_get_new_organism/0
select/0
Bio.GA.Selection.RouletteWheel
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Bio.GA.Selection.RouletteWheel.RouletteWheelSelection
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Summary
Functions
__init__/0
_set_up_wheel/0
select/0
Bio.GA.Selection.Tournament
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Bio.GA.Selection.Tournament.TournamentSelection
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Summary
Functions
__init__/0
select/0
Bio.GenBank.Record
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Summary
Functions
_indent_genbank/0
_wrapped_genbank/0
Bio.GenBank.Record.Feature
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Summary
Functions
__init__/0
__str__/0
Bio.GenBank.Record.Qualifier
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Summary
Functions
__init__/0
Bio.GenBank.Record.Record
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Summary
Functions
__init__/0
__str__/0
_accession_line/0
_base_count_line/0
_comment_line/0
_contig_line/0
_db_source_line/0
_definition_line/0
_features_line/0
_keywords_line/0
_locus_line/0
_nid_line/0
_organism_line/0
_origin_line/0
_pid_line/0
_segment_line/0
_sequence_line/0
_source_line/0
_version_line/0
Bio.GenBank.Record.Reference
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Summary
Functions
__init__/0
__str__/0
_authors_line/0
_consrtm_line/0
_journal_line/0
_medline_line/0
_pubmed_line/0
_reference_line/0
_remark_line/0
_title_line/0
Bio.GenBank.Scanner
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Bio.GenBank.Scanner.EmblScanner
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Summary
Functions
_feed_first_line_new/0
_feed_first_line_old/0
_feed_first_line_patents_kipo/0
parse_footer/0
Bio.Geo.Record
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Bio.Geo.Record.Record
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Summary
Functions
__init__/0
Bio.Graphics.BasicChromosome
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Summary
Functions
_spring_layout/0
Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment
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Summary
Functions
__init__/0
_overdraw_subcomponents/0
Bio.Graphics.BasicChromosome.Chromosome
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Summary
Functions
__init__/0
_draw_label/0
_draw_labels/0
draw/0
subcomponent_size/0
Bio.Graphics.BasicChromosome.ChromosomeSegment
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Summary
Functions
__init__/0
_draw_label/0
_draw_segment/0
_draw_subcomponents/0
_overdraw_subcomponents/0
draw/0
Bio.Graphics.BasicChromosome.Organism
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Summary
Functions
__init__/0
_draw_legend/0
_draw_title/0
draw/0
Bio.Graphics.BasicChromosome.SpacerSegment
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Summary
Functions
draw/0
Bio.Graphics.BasicChromosome.TelomereSegment
Top
Summary
Functions
__init__/0
_draw_segment/0
Bio.Graphics.ColorSpiral
Top
Summary
Functions
get_color_dict/0
get_colors/0
Bio.Graphics.ColorSpiral.ColorSpiral
Top
Summary
Functions
__init__/0
get_colors/0
Bio.Graphics.Comparative
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Bio.Graphics.Comparative.ComparativeScatterPlot
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Summary
Functions
__init__/0
_draw_scatter_plot/0
_draw_title/0
_find_min_max/0
_set_colors_and_shapes/0
draw_to_file/0
Bio.Graphics.DisplayRepresentation
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Bio.Graphics.DisplayRepresentation.ChromosomeCounts
Top
Summary
Functions
__init__/0
_color_from_count/0
add_count/0
add_label/0
fill_chromosome/0
get_segment_info/0
scale_segment_value/0
set_scale/0
Bio.Graphics.Distribution
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Bio.Graphics.Distribution.BarChartDistribution
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Summary
Functions
__init__/0
_determine_position/0
_draw_title/0
draw/0
Bio.Graphics.Distribution.DistributionPage
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Summary
Functions
__init__/0
_draw_distributions/0
_draw_legend/0
_draw_title/0
draw/0
Bio.Graphics.Distribution.LineDistribution
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Summary
Functions
__init__/0
draw/0
Bio.Graphics.KGML_vis
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Summary
Functions
color_to_reportlab/0
darken/0
get_temp_imagefilename/0
Bio.Graphics.KGML_vis.KGMLCanvas
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Summary
Functions
__add_compounds/0
__add_genes/0
__add_graphics/0
__add_labels/0
__add_maps/0
__add_orthologs/0
__add_reaction_entries/0
__add_relations/0
__draw_arrow/0
__init__/0
draw/0
Bio.HMM.DynamicProgramming
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Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
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Summary
Functions
__init__/0
_backward_recursion/0
_forward_recursion/0
backward_algorithm/0
forward_algorithm/0
Bio.HMM.DynamicProgramming.LogDPAlgorithms
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Summary
Functions
__init__/0
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
Top
Summary
Functions
__init__/0
_backward_recursion/0
_calculate_s_value/0
_forward_recursion/0
Bio.HMM.MarkovModel
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Summary
Functions
_calculate_emissions/0
_calculate_from_transitions/0
_calculate_to_transitions/0
_gen_random_array/0
Bio.HMM.MarkovModel.HiddenMarkovModel
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Summary
Functions
__init__/0
_log_transform/0
get_blank_emissions/0
get_blank_transitions/0
transitions_from/0
transitions_to/0
viterbi/0
Bio.HMM.MarkovModel.MarkovModelBuilder
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Summary
Functions
__init__/0
_all_blank/0
_all_pseudo/0
allow_all_transitions/0
allow_transition/0
destroy_transition/0
get_markov_model/0
set_emission_pseudocount/0
set_emission_score/0
set_equal_probabilities/0
set_initial_probabilities/0
set_random_emission_probabilities/0
set_random_initial_probabilities/0
set_random_probabilities/0
set_random_transition_probabilities/0
set_transition_pseudocount/0
set_transition_score/0
Bio.HMM.Trainer
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Bio.HMM.Trainer.AbstractTrainer
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Summary
Functions
__init__/0
estimate_params/0
log_likelihood/0
ml_estimator/0
Bio.HMM.Trainer.BaumWelchTrainer
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Summary
Functions
__init__/0
train/0
update_emissions/0
update_transitions/0
Bio.HMM.Trainer.KnownStateTrainer
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Summary
Functions
__init__/0
_count_emissions/0
_count_transitions/0
train/0
Bio.HMM.Trainer.TrainingSequence
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Summary
Functions
__init__/0
Bio.HMM.Utilities
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Summary
Functions
pretty_print_prediction/0
Bio.Index
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Bio.KDTree.KDTree
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Bio.KDTree.KDTree.KDTree
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Summary
Functions
__init__/0
all_get_indices/0
all_get_radii/0
all_search/0
get_indices/0
get_radii/0
search/0
set_coords/0
Bio.KEGG.KGML.KGML_parser
Top
Summary
Functions
parse/0
read/0
Bio.KEGG.KGML.KGML_parser.KGMLParser
Top
Summary
Functions
__init__/0
parse/0
Bio.KEGG.KGML.KGML_pathway
Top
Bio.KEGG.KGML.KGML_pathway.Component
Top
Summary
Functions
__init__/0
element/0
Bio.KEGG.KGML.KGML_pathway.Entry
Top
Summary
Functions
__init__/0
__str__/0
add_component/0
add_graphics/0
bounds/0
element/0
is_reactant/0
remove_component/0
remove_graphics/0
Bio.KEGG.KGML.KGML_pathway.Graphics
Top
Summary
Functions
__init__/0
bounds/0
centre/0
element/0
Bio.KEGG.KGML.KGML_pathway.Pathway
Top
Summary
Functions
__init__/0
__str__/0
add_entry/0
add_reaction/0
add_relation/0
bounds/0
compounds/0
element/0
genes/0
get_KGML/0
maps/0
orthologs/0
reaction_entries/0
reactions/0
relations/0
remove_entry/0
remove_reaction/0
remove_relation/0
Bio.KEGG.KGML.KGML_pathway.Reaction
Top
Summary
Functions
__init__/0
__str__/0
add_product/0
add_substrate/0
element/0
entry/0
products/0
reactant_ids/0
substrates/0
Bio.KEGG.KGML.KGML_pathway.Relation
Top
Summary
Functions
__init__/0
__str__/0
element/0
Bio.KEGG.REST
Top
Summary
Functions
kegg_conv/0
kegg_find/0
kegg_get/0
kegg_info/0
kegg_link/0
kegg_list/0
Bio.LogisticRegression
Top
Summary
Functions
calculate/0
classify/0
train/0
Bio.LogisticRegression.LogisticRegression
Top
Summary
Functions
__init__/0
Bio.MarkovModel
Top
Summary
Functions
_argmaxes/0
_backward/0
_baum_welch/0
_baum_welch_one/0
_copy_and_check/0
_exp_logsum/0
_forward/0
_logsum/0
_logvecadd/0
_mle/0
_normalize/0
_random_norm/0
_readline_and_check_start/0
_uniform_norm/0
_viterbi/0
find_states/0
itemindex/0
load/0
logaddexp/0
save/0
train_bw/0
train_visible/0
Bio.MarkovModel.MarkovModel
Top
Summary
Functions
__init__/0
__str__/0
Bio.NMR.NOEtools
Top
Summary
Functions
predictNOE/0
Bio.NaiveBayes
Top
Summary
Functions
_contents/0
calculate/0
classify/0
train/0
Bio.NaiveBayes.NaiveBayes
Top
Summary
Functions
__init__/0
Bio.NeuralNetwork.BackPropagation.Layer
Top
Summary
Functions
logistic_function/0
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer
Top
Summary
Functions
__init__/0
__str__/0
set_weight/0
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer
Top
Summary
Functions
__init__/0
backpropagate/0
update/0
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer
Top
Summary
Functions
__init__/0
backpropagate/0
update/0
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
Top
Summary
Functions
__init__/0
backpropagate/0
get_error/0
update/0
Bio.NeuralNetwork.BackPropagation.Network
Top
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
Top
Summary
Functions
__init__/0
predict/0
train/0
Bio.NeuralNetwork.Gene.Motif
Top
Bio.NeuralNetwork.Gene.Motif.MotifCoder
Top
Summary
Functions
__init__/0
representation/0
Bio.NeuralNetwork.Gene.Motif.MotifFinder
Top
Summary
Functions
__init__/0
_add_motif/0
_get_motif_dict/0
find/0
find_differences/0
Bio.NeuralNetwork.Gene.Pattern
Top
Bio.NeuralNetwork.Gene.Pattern.PatternIO
Top
Summary
Functions
__init__/0
read/0
write/0
write_seq/0
Bio.NeuralNetwork.Gene.Pattern.PatternRepository
Top
Summary
Functions
__init__/0
count/0
get_all/0
get_differing/0
get_random/0
get_top/0
get_top_percentage/0
remove_polyA/0
Bio.NeuralNetwork.Gene.Schema
Top
Summary
Functions
matches_schema/0
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness
Top
Summary
Functions
__init__/0
calculate_fitness/0
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder
Top
Summary
Functions
__init__/0
_set_up_genetic_algorithm/0
find_schemas/0
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness
Top
Summary
Functions
__init__/0
calculate_fitness/0
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator
Top
Summary
Functions
__init__/0
random_motif/0
Bio.NeuralNetwork.Gene.Schema.Schema
Top
Summary
Functions
__init__/0
all_unambiguous/0
encode_motif/0
find_ambiguous/0
find_matches/0
num_ambiguous/0
num_matches/0
Bio.NeuralNetwork.Gene.Schema.SchemaCoder
Top
Summary
Functions
__init__/0
representation/0
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet
Top
Bio.NeuralNetwork.Gene.Schema.SchemaFactory
Top
Summary
Functions
__init__/0
_get_num_motifs/0
_get_unique_schema/0
_schema_from_motif/0
from_motifs/0
from_signatures/0
Bio.NeuralNetwork.Gene.Schema.SchemaFinder
Top
Summary
Functions
__init__/0
find/0
find_differences/0
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher
Top
Summary
Functions
__init__/0
is_finished/0
Bio.NeuralNetwork.Gene.Signature
Top
Bio.NeuralNetwork.Gene.Signature.SignatureCoder
Top
Summary
Functions
__init__/0
representation/0
Bio.NeuralNetwork.Gene.Signature.SignatureFinder
Top
Summary
Functions
__init__/0
_add_sig/0
_get_signature_dict/0
find/0
Bio.NeuralNetwork.StopTraining
Top
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop
Top
Summary
Functions
__init__/0
stopping_criteria/0
Bio.NeuralNetwork.Training
Top
Bio.NeuralNetwork.Training.ExampleManager
Top
Summary
Functions
__init__/0
add_examples/0
Bio.NeuralNetwork.Training.TrainingExample
Top
Summary
Functions
__init__/0
Bio.Nexus.Nexus
Top
Summary
Functions
_adjust_lines/0
_compact4nexus/0
_kill_comments_and_break_lines/0
_make_unique/0
_replace_parenthesized_ambigs/0
_seqmatrix2strmatrix/0
_sort_keys_by_values/0
_unique_label/0
combine/0
get_start_end/0
quotestrip/0
safename/0
Bio.Nexus.Nexus.Block
Top
Summary
Functions
__init__/0
Bio.Nexus.Nexus.CharBuffer
Top
Summary
Functions
__init__/0
__next__/0
next/0
next_nonwhitespace/0
next_until/0
next_word/0
peek_word/0
rest/0
skip_whitespace/0
Bio.Nexus.Nexus.Commandline
Top
Summary
Functions
__init__/0
Bio.Nexus.Nexus.Nexus
Top
Summary
Functions
__init__/0
_adjust/0
_adjust_charlabels/0
_apply_block_structure/0
_charlabels/0
_charpartition/0
_charset/0
_check_taxlabels/0
_codonposset/0
_get_indices/0
_get_nexus_block/0
_matrix/0
_name_n_vector/0
_parse_list/0
_parse_nexus_block/0
_resolve/0
_taxlabels/0
_taxpartition/0
_taxset/0
_translate/0
_utree/0
add_sequence/0
append_sets/0
bootstrap/0
constant/0
crop_matrix/0
cstatus/0
export_fasta/0
export_phylip/0
gaponly/0
get_original_taxon_order/0
insert_gap/0
invert/0
read/0
set_original_taxon_order/0
terminal_gap_to_missing/0
weighted_stepmatrix/0
write_nexus_data/0
write_nexus_data_partitions/0
Bio.Nexus.Nexus.NexusError
Top
Bio.Nexus.Nexus.StepMatrix
Top
Summary
Functions
__init__/0
set/0
smprint/0
Bio.Nexus.Nodes
Top
Bio.Nexus.Nodes.Chain
Top
Summary
Functions
__init__/0
_get_id/0
add/0
all_ids/0
collapse/0
is_parent_of/0
kill/0
link/0
trace/0
unlink/0
Bio.Nexus.Nodes.ChainException
Top
Bio.Nexus.Nodes.Node
Top
Summary
Functions
__init__/0
add_succ/0
get_data/0
get_id/0
get_prev/0
get_succ/0
remove_succ/0
set_data/0
set_id/0
set_prev/0
set_succ/0
Bio.Nexus.Nodes.NodeException
Top
Bio.Nexus.StandardData
Top
Bio.Nexus.StandardData.NexusError
Top
Bio.Nexus.StandardData.StandardData
Top
Summary
Functions
__init__/0
__len__/0
__str__/0
next/0
raw/0
Bio.Nexus.Trees
Top
Summary
Functions
consensus/0
Bio.Nexus.Trees.NodeData
Top
Summary
Functions
__init__/0
Bio.Nexus.Trees.Tree
Top
Summary
Functions
__init__/0
__str__/0
_add_nodedata/0
_add_subtree/0
_connect_subtree/0
_get_values/0
_parse/0
_walk/0
branchlength2support/0
collapse_genera/0
common_ancestor/0
convert_absolute_support/0
count_terminals/0
display/0
distance/0
get_taxa/0
get_terminals/0
has_support/0
is_bifurcating/0
is_compatible/0
is_identical/0
is_internal/0
is_monophyletic/0
is_preterminal/0
is_terminal/0
ladderize_nodes/0
make_info_string/0
merge_with_support/0
newickize/0
node/0
prune/0
randomize/0
search_taxon/0
set_subtree/0
split/0
sum_branchlength/0
to_string/0
unroot/0
Bio.Nexus.Trees.TreeError
Top
Bio.PDB.AbstractPropertyMap
Top
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap
Top
Summary
Functions
__init__/0
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap
Top
Summary
Functions
__contains__/0
__getitem__/0
__init__/0
__iter__/0
__len__/0
has_key/0
keys/0
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap
Top
Summary
Functions
__init__/0
Bio.PDB.Atom
Top
Bio.PDB.Atom.Atom
Top
Summary
Functions
__init__/0
__repr__/0
__sub__/0
_assign_element/0
copy/0
detach_parent/0
flag_disorder/0
get_altloc/0
get_anisou/0
get_bfactor/0
get_coord/0
get_full_id/0
get_fullname/0
get_id/0
get_name/0
get_occupancy/0
get_parent/0
get_sigatm/0
get_siguij/0
get_vector/0
is_disordered/0
set_anisou/0
set_parent/0
set_sigatm/0
set_siguij/0
transform/0
Bio.PDB.Atom.DisorderedAtom
Top
Summary
Functions
__init__/0
disordered_add/0
Bio.PDB.Chain
Top
Bio.PDB.Chain.Chain
Top
Summary
Functions
__contains__/0
__delitem__/0
__getitem__/0
__init__/0
_translate_id/0
get_unpacked_list/0
has_id/0
Bio.PDB.DSSP.DSSP
Top
Summary
Functions
__init__/0
resid2code/0
Bio.PDB.Dice
Top
Summary
Functions
extract/0
Bio.PDB.Dice.ChainSelector
Top
Summary
Functions
__init__/0
Bio.PDB.Entity
Top
Bio.PDB.Entity.DisorderedEntityWrapper
Top
Summary
Functions
__contains__/0
__getattr__/0
__getitem__/0
__init__/0
__iter__/0
__len__/0
__setitem__/0
__sub__/0
detach_parent/0
disordered_add/0
disordered_get/0
disordered_get_id_list/0
disordered_get_list/0
disordered_has_id/0
disordered_select/0
get_id/0
get_parent/0
is_disordered/0
set_parent/0
Bio.PDB.Entity.Entity
Top
Summary
Functions
__contains__/0
__delitem__/0
__getitem__/0
__init__/0
__iter__/0
__len__/0
_reset_full_id/0
add/0
detach_child/0
detach_parent/0
get_full_id/0
get_id/0
get_iterator/0
get_level/0
get_list/0
get_parent/0
has_id/0
id/0
insert/0
set_parent/0
transform/0
Bio.PDB.FragmentMapper
Top
Summary
Functions
_make_fragment_list/0
_map_fragment_list/0
_read_fragments/0
Bio.PDB.FragmentMapper.Fragment
Top
Summary
Functions
__init__/0
__len__/0
__repr__/0
__sub__/0
add_residue/0
get_coords/0
get_id/0
get_resname_list/0
Bio.PDB.FragmentMapper.FragmentMapper
Top
Summary
Functions
__contains__/0
__getitem__/0
__init__/0
_map/0
has_key/0
Bio.PDB.HSExposure
Top
Bio.PDB.HSExposure.ExposureCN
Top
Summary
Functions
__init__/0
Bio.PDB.HSExposure.HSExposureCA
Top
Summary
Functions
__init__/0
_get_cb/0
pcb_vectors_pymol/0
Bio.PDB.HSExposure.HSExposureCB
Top
Summary
Functions
__init__/0
_get_cb/0
Bio.PDB.MMCIF2Dict
Top
Bio.PDB.MMCIF2Dict.MMCIF2Dict
Top
Summary
Functions
__init__/0
Bio.PDB.MMCIFParser
Top
Bio.PDB.MMCIFParser.FastMMCIFParser
Top
Summary
Functions
__init__/0
get_structure/0
Bio.PDB.MMCIFParser.MMCIFParser
Top
Summary
Functions
__init__/0
get_structure/0
Bio.PDB.Model
Top
Bio.PDB.Model.Model
Top
Summary
Functions
__init__/0
Bio.PDB.NACCESS
Top
Bio.PDB.NACCESS.NACCESS
Top
Summary
Functions
__init__/0
Bio.PDB.NeighborSearch
Top
Bio.PDB.NeighborSearch.NeighborSearch
Top
Summary
Functions
__init__/0
search/0
search_all/0
Bio.PDB.PDBExceptions
Top
Bio.PDB.PDBExceptions.PDBConstructionException
Top
Bio.PDB.PDBExceptions.PDBConstructionWarning
Top
Bio.PDB.PDBExceptions.PDBException
Top
Bio.PDB.PDBIO
Top
Bio.PDB.PDBIO.PDBIO
Top
Summary
Functions
__init__/0
_get_atom_line/0
save/0
Bio.PDB.PDBIO.Select
Top
Summary
Functions
accept_atom/0
accept_chain/0
accept_model/0
accept_residue/0
Bio.PDB.PDBList
Top
Bio.PDB.PDBParser
Top
Bio.PDB.PDBParser.PDBParser
Top
Summary
Functions
__init__/0
_get_header/0
_handle_PDB_exception/0
_parse/0
_parse_coordinates/0
get_header/0
get_structure/0
get_trailer/0
Bio.PDB.PSEA
Top
Summary
Functions
annotate/0
psea/0
psea2HEC/0
run_psea/0
Bio.PDB.PSEA.PSEA
Top
Summary
Functions
__init__/0
get_seq/0
Bio.PDB.Polypeptide
Top
Summary
Functions
index_to_one/0
index_to_three/0
is_aa/0
one_to_index/0
one_to_three/0
three_to_index/0
three_to_one/0
Bio.PDB.Polypeptide.CaPPBuilder
Top
Summary
Functions
__init__/0
Bio.PDB.Polypeptide.PPBuilder
Top
Summary
Functions
__init__/0
_test_dist/0
Bio.PDB.Polypeptide.Polypeptide
Top
Summary
Functions
__repr__/0
get_ca_list/0
get_phi_psi_list/0
get_sequence/0
get_tau_list/0
get_theta_list/0
Bio.PDB.Residue
Top
Bio.PDB.Residue.DisorderedResidue
Top
Summary
Functions
__init__/0
disordered_add/0
sort/0
Bio.PDB.Residue.Residue
Top
Summary
Functions
__init__/0
add/0
flag_disordered/0
get_unpacked_list/0
is_disordered/0
sort/0
Bio.PDB.ResidueDepth
Top
Summary
Functions
_get_atom_radius/0
_read_vertex_array/0
get_surface/0
min_dist/0
residue_depth/0
Bio.PDB.ResidueDepth.ResidueDepth
Top
Summary
Functions
__init__/0
Bio.PDB.Selection
Top
Summary
Functions
get_unique_parents/0
unfold_entities/0
uniqueify/0
Bio.PDB.Structure
Top
Bio.PDB.Structure.Structure
Top
Summary
Functions
__init__/0
Bio.PDB.StructureAlignment
Top
Bio.PDB.StructureAlignment.StructureAlignment
Top
Summary
Functions
__init__/0
_test_equivalence/0
get_iterator/0
get_maps/0
Bio.PDB.StructureBuilder
Top
Bio.PDB.StructureBuilder.StructureBuilder
Top
Summary
Functions
__init__/0
_is_completely_disordered/0
get_structure/0
init_atom/0
init_chain/0
init_model/0
init_residue/0
init_seg/0
init_structure/0
set_anisou/0
set_line_counter/0
set_sigatm/0
set_siguij/0
Bio.PDB.Superimposer
Top
Bio.PDB.Superimposer.Superimposer
Top
Summary
Functions
__init__/0
apply/0
set_atoms/0
Bio.PDB.Vector
Top
Summary
Functions
calc_angle/0
calc_dihedral/0
m2rotaxis/0
refmat/0
rotaxis2m/0
rotmat/0
vector_to_axis/0
Bio.PDB.Vector.Vector
Top
Summary
Functions
__add__/0
__div__/0
__init__/0
__mul__/0
__neg__/0
__pow__/0
__sub__/0
angle/0
copy/0
get_array/0
left_multiply/0
norm/0
normalize/0
normalized/0
normsq/0
right_multiply/0
Bio.ParserSupport
Top
Summary
Functions
attempt_read_and_call/0
is_blank_line/0
read_and_call/0
read_and_call_until/0
read_and_call_while/0
safe_peekline/0
safe_readline/0
Bio.ParserSupport.AbstractConsumer
Top
Bio.ParserSupport.AbstractParser
Top
Bio.ParserSupport.TaggingConsumer
Top
Summary
Functions
__init__/0
Bio.Pathway.Rep.Graph
Top
Bio.Pathway.Rep.Graph.Graph
Top
Summary
Functions
__eq__/0
__init__/0
__ne__/0
__repr__/0
__str__/0
add_edge/0
add_node/0
child_edges/0
children/0
edges/0
labels/0
nodes/0
parent_edges/0
parents/0
remove_edge/0
remove_node/0
Bio.Pathway.Rep.MultiGraph
Top
Summary
Functions
bf_search/0
df_search/0
Bio.Pathway.Rep.MultiGraph.MultiGraph
Top
Summary
Functions
__eq__/0
__init__/0
__ne__/0
__repr__/0
__str__/0
add_edge/0
add_node/0
child_edges/0
children/0
edges/0
labels/0
nodes/0
parent_edges/0
parents/0
remove_edge/0
remove_node/0
Bio.Phylo.BaseTree
Top
Summary
Functions
_attribute_matcher/0
_class_matcher/0
_combine_args/0
_combine_matchers/0
_function_matcher/0
_identity_matcher/0
_level_traverse/0
_object_matcher/0
_postorder_traverse/0
_preorder_traverse/0
_sorted_attrs/0
as_string/0
Bio.Phylo.BaseTree.BranchColor
Top
Summary
Functions
__init__/0
__repr__/0
__str__/0
from_hex/0
from_name/0
to_hex/0
to_rgb/0
Bio.Phylo.BaseTree.Clade
Top
Summary
Functions
__bool__/0
__getitem__/0
__init__/0
__iter__/0
__len__/0
__str__/0
is_terminal/0
root/0
Bio.Phylo.BaseTree.Tree
Top
Summary
Functions
__format__/0
__init__/0
__str__/0
as_phyloxml/0
clade/0
format/0
from_clade/0
is_terminal/0
print_tree/0
randomized/0
root_at_midpoint/0
root_with_outgroup/0
Bio.Phylo.BaseTree.TreeElement
Top
Summary
Functions
__repr__/0
Bio.Phylo.BaseTree.TreeMixin
Top
Summary
Functions
_filter_search/0
collapse/0
collapse_all/0
common_ancestor/0
count_terminals/0
depths/0
distance/0
find_any/0
find_clades/0
find_elements/0
get_nonterminals/0
get_path/0
get_terminals/0
is_bifurcating/0
is_monophyletic/0
is_parent_of/0
is_preterminal/0
ladderize/0
prune/0
split/0
total_branch_length/0
trace/0
Bio.Phylo.CDAO
Top
Bio.Phylo.CDAO.Clade
Top
Summary
Functions
__init__/0
Bio.Phylo.CDAO.Tree
Top
Summary
Functions
__init__/0
Bio.Phylo.CDAOIO
Top
Summary
Functions
format_label/0
parse/0
qUri/0
write/0
Bio.Phylo.CDAOIO.CDAOError
Top
Bio.Phylo.CDAOIO.Parser
Top
Summary
Functions
__init__/0
from_string/0
get_node_info/0
new_clade/0
parse/0
parse_children/0
parse_graph/0
parse_handle_to_graph/0
Bio.Phylo.CDAOIO.Writer
Top
Summary
Functions
__init__/0
add_stmt_to_handle/0
process_clade/0
write/0
Bio.Phylo.Consensus
Top
Summary
Functions
_bitstring_topology/0
_clade_to_bitstr/0
_count_clades/0
_equal_topology/0
_part/0
_sub_clade/0
_tree_to_bitstrs/0
adam_consensus/0
bootstrap/0
bootstrap_consensus/0
bootstrap_trees/0
get_support/0
majority_consensus/0
strict_consensus/0
Bio.Phylo.NeXML
Top
Bio.Phylo.NeXML.Clade
Top
Summary
Functions
__init__/0
Bio.Phylo.NeXML.Tree
Top
Summary
Functions
__init__/0
Bio.Phylo.NeXMLIO
Top
Summary
Functions
cdao_to_obo/0
matches/0
parse/0
qUri/0
write/0
Bio.Phylo.NeXMLIO.NeXMLError
Top
Bio.Phylo.NeXMLIO.Parser
Top
Summary
Functions
__init__/0
_make_tree/0
add_annotation/0
from_string/0
parse/0
Bio.Phylo.NeXMLIO.Writer
Top
Summary
Functions
__init__/0
_write_tree/0
new_label/0
write/0
Bio.Phylo.Newick
Top
Bio.Phylo.Newick.Clade
Top
Summary
Functions
__init__/0
Bio.Phylo.Newick.Tree
Top
Summary
Functions
__init__/0
Bio.Phylo.NewickIO
Top
Summary
Functions
parse/0
write/0
Bio.Phylo.NewickIO.NewickError
Top
Bio.Phylo.NewickIO.Parser
Top
Summary
Functions
__init__/0
_parse_tree/0
from_string/0
new_clade/0
parse/0
process_clade/0
Bio.Phylo.NewickIO.Writer
Top
Summary
Functions
__init__/0
_info_factory/0
newickize/0
to_strings/0
write/0
Bio.Phylo.PhyloXML
Top
Summary
Functions
_check_str/0
Bio.Phylo.PhyloXML.Accession
Top
Summary
Functions
__init__/0
__str__/0
Bio.Phylo.PhyloXML.Annotation
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.BinaryCharacters
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.BranchColor
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.Clade
Top
Summary
Functions
__init__/0
from_clade/0
to_phylogeny/0
Bio.Phylo.PhyloXML.CladeRelation
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.Confidence
Top
Summary
Functions
__abs__/0
__add__/0
__div__/0
__eq__/0
__float__/0
__floordiv__/0
__hash__/0
__init__/0
__int__/0
__long__/0
__mod__/0
__mul__/0
__ne__/0
__neg__/0
__sub__/0
__truediv__/0
Bio.Phylo.PhyloXML.Date
Top
Summary
Functions
__init__/0
__str__/0
Bio.Phylo.PhyloXML.Distribution
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.DomainArchitecture
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.Events
Top
Summary
Functions
__init__/0
__iter__/0
values/0
Bio.Phylo.PhyloXML.Id
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.MolSeq
Top
Summary
Functions
__init__/0
__str__/0
Bio.Phylo.PhyloXML.Other
Top
Summary
Functions
__init__/0
__iter__/0
Bio.Phylo.PhyloXML.PhyloElement
Top
Bio.Phylo.PhyloXML.PhyloXMLWarning
Top
Bio.Phylo.PhyloXML.Phylogeny
Top
Summary
Functions
__init__/0
_get_confidence/0
as_phyloxml/0
from_clade/0
from_tree/0
to_alignment/0
to_phyloxml_container/0
Bio.Phylo.PhyloXML.Phyloxml
Top
Summary
Functions
__getitem__/0
__init__/0
__iter__/0
__len__/0
__str__/0
Bio.Phylo.PhyloXML.Point
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.Polygon
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.Property
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.ProteinDomain
Top
Summary
Functions
__init__/0
to_seqfeature/0
Bio.Phylo.PhyloXML.Reference
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.Sequence
Top
Summary
Functions
__init__/0
clean_dict/0
from_seqrecord/0
to_seqrecord/0
Bio.Phylo.PhyloXML.SequenceRelation
Top
Summary
Functions
__init__/0
Bio.Phylo.PhyloXML.Taxonomy
Top
Summary
Functions
__init__/0
__str__/0
Bio.Phylo.PhyloXMLIO
Top
Summary
Functions
_clean_attrib/0
_collapse_wspace/0
_get_child_as/0
_get_child_text/0
_get_children_as/0
_get_children_text/0
_indent/0
_local/0
_ns/0
_replace_wspace/0
_serialize/0
_split_namespace/0
parse/0
read/0
write/0
Bio.Phylo.PhyloXMLIO.Parser
Top
Summary
Functions
__init__/0
_parse_clade/0
_parse_phylogeny/0
parse/0
read/0
Bio.Phylo.PhyloXMLIO.PhyloXMLError
Top
Bio.Phylo.PhyloXMLIO.Writer
Top
Summary
Functions
__init__/0
binary_characters/0
domain/0
Bio.Phylo.TreeConstruction
Top
Bio.Phylo.TreeConstruction.DistanceCalculator
Top
Summary
Functions
__init__/0
_build_protein_matrix/0
_pairwise/0
get_distance/0
Bio.Phylo.TreeConstruction.DistanceMatrix
Top
Summary
Functions
__init__/0
_set_zero_diagonal/0
format_phylip/0
Bio.Phylo.TreeConstruction.DistanceTreeConstructor
Top
Summary
Functions
__init__/0
_height_of/0
nj/0
upgma/0
Bio.Phylo.TreeConstruction.NNITreeSearcher
Top
Summary
Functions
__init__/0
_get_neighbors/0
_nni/0
search/0
Bio.Phylo.TreeConstruction.ParsimonyScorer
Top
Summary
Functions
__init__/0
get_score/0
Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor
Top
Summary
Functions
__init__/0
build_tree/0
Bio.Phylo.TreeConstruction.Scorer
Top
Summary
Functions
get_score/0
Bio.Phylo.TreeConstruction.TreeConstructor
Top
Summary
Functions
build_tree/0
Bio.Phylo.TreeConstruction.TreeSearcher
Top
Summary
Functions
search/0
Bio.PopGen.GenePop.Controller
Top
Summary
Functions
_gp_float/0
_gp_int/0
Bio.PopGen.GenePop.Controller.GenePopController
Top
Summary
Functions
__init__/0
_calc_ibd/0
_test_global_hz_both/0
_test_pop_hz_both/0
calc_allele_genotype_freqs/0
calc_fst_all/0
calc_ibd_diplo/0
calc_ibd_haplo/0
test_global_hz_deficiency/0
test_global_hz_excess/0
test_pop_hz_deficiency/0
test_pop_hz_excess/0
test_pop_hz_prob/0
Bio.PopGen.GenePop.EasyController
Top
Bio.PopGen.GenePop.EasyController.EasyController
Top
Summary
Functions
__init__/0
estimate_nm/0
get_alleles/0
get_alleles_all_pops/0
get_f_stats/0
get_fis/0
get_genotype_count/0
get_heterozygosity_info/0
get_multilocus_f_stats/0
Bio.PopGen.GenePop.FileParser
Top
Summary
Functions
read/0
Bio.PopGen.GenePop.FileParser.FileRecord
Top
Summary
Functions
__init__/0
__str__/0
get_individual/0
remove_loci_by_name/0
remove_loci_by_position/0
remove_locus_by_name/0
remove_locus_by_position/0
remove_population/0
seek_position/0
skip_header/0
skip_population/0
start_read/0
Bio.PopGen.GenePop.LargeFileParser
Top
Summary
Functions
read/0
Bio.PopGen.GenePop.LargeFileParser.Record
Top
Summary
Functions
__init__/0
Bio.PopGen.GenePop.Utils
Top
Bio.Restriction.PrintFormat.PrintFormat
Top
Summary
Functions
__init__/0
__next_section/0
_make_list/0
_make_list_only/0
_make_map/0
_make_map_only/0
_make_nocut/0
_make_nocut_only/0
_make_number/0
_make_number_only/0
format_output/0
make_format/0
print_as/0
print_that/0
Bio.Restriction.RanaConfig
Top
Bio.Restriction.Restriction
Top
Summary
Functions
_check_bases/0
Bio.Restriction.Restriction.AbstractCut
Top
Summary
Functions
all_suppliers/0
equischizomers/0
frequency/0
is_equischizomer/0
is_isoschizomer/0
is_neoschizomer/0
isoschizomers/0
neoschizomers/0
search/0
Bio.Restriction.Restriction.Ambiguous
Top
Summary
Functions
_drop/0
_mod2/0
elucidate/0
is_ambiguous/0
is_defined/0
is_unknown/0
Bio.Restriction.Restriction.Analysis
Top
Summary
Functions
__init__/0
_boundaries/0
_sub_set/0
_test_normal/0
_test_reverse/0
between/0
blunt/0
change/0
defined/0
do_not_cut/0
format_output/0
full/0
only_between/0
only_outside/0
outside/0
overhang3/0
overhang5/0
print_that/0
show_only_between/0
with_N_sites/0
with_name/0
with_number_list/0
with_site_size/0
with_sites/0
without_site/0
Bio.Restriction.Restriction.Blunt
Top
Summary
Functions
_mod1/0
catalyse/0
compatible_end/0
is_3overhang/0
is_5overhang/0
is_blunt/0
overhang/0
Bio.Restriction.Restriction.Commercially_available
Top
Summary
Functions
buffers/0
is_comm/0
supplier_list/0
suppliers/0
Bio.Restriction.Restriction.Defined
Top
Summary
Functions
_drop/0
_mod2/0
elucidate/0
is_ambiguous/0
is_defined/0
is_unknown/0
Bio.Restriction.Restriction.FormattedSeq
Top
Summary
Functions
__init__/0
circularise/0
finditer/0
is_linear/0
linearise/0
to_circular/0
to_linear/0
Bio.Restriction.Restriction.Meth_Dep
Top
Summary
Functions
is_methylable/0
Bio.Restriction.Restriction.Meth_Undep
Top
Summary
Functions
is_methylable/0
Bio.Restriction.Restriction.NoCut
Top
Summary
Functions
_modify/0
_rev_modify/0
characteristic/0
cut_once/0
cut_twice/0
Bio.Restriction.Restriction.NonPalindromic
Top
Summary
Functions
_search/0
is_palindromic/0
Bio.Restriction.Restriction.NotDefined
Top
Summary
Functions
_drop/0
_mod2/0
elucidate/0
is_ambiguous/0
is_defined/0
is_unknown/0
Bio.Restriction.Restriction.Not_available
Top
Summary
Functions
buffers/0
is_comm/0
supplier_list/0
suppliers/0
Bio.Restriction.Restriction.OneCut
Top
Summary
Functions
_modify/0
_rev_modify/0
characteristic/0
cut_once/0
cut_twice/0
Bio.Restriction.Restriction.Ov3
Top
Summary
Functions
_mod1/0
catalyse/0
compatible_end/0
is_3overhang/0
is_5overhang/0
is_blunt/0
overhang/0
Bio.Restriction.Restriction.Ov5
Top
Summary
Functions
_mod1/0
catalyse/0
compatible_end/0
is_3overhang/0
is_5overhang/0
is_blunt/0
overhang/0
Bio.Restriction.Restriction.Palindromic
Top
Summary
Functions
_search/0
is_palindromic/0
Bio.Restriction.Restriction.RestrictionBatch
Top
Summary
Functions
__add__/0
__div__/0
__iadd__/0
__init__/0
__rdiv__/0
__rtruediv__/0
__truediv__/0
add/0
add_nocheck/0
add_supplier/0
as_string/0
current_suppliers/0
elements/0
format/0
get/0
is_restriction/0
lambdasplit/0
remove/0
search/0
show_codes/0
split/0
suppl_codes/0
Bio.Restriction.Restriction.RestrictionType
Top
Summary
Functions
__add__/0
__div__/0
__eq__/0
__floordiv__/0
__ge__/0
__gt__/0
__init__/0
__le__/0
__len__/0
__lt__/0
__mod__/0
__ne__/0
__rdiv__/0
__repr__/0
__rfloordiv__/0
__rshift__/0
__rtruediv__/0
__str__/0
__truediv__/0
Bio.Restriction.Restriction.TwoCuts
Top
Summary
Functions
_modify/0
_rev_modify/0
characteristic/0
cut_once/0
cut_twice/0
Bio.Restriction.Restriction.Unknown
Top
Summary
Functions
_mod1/0
catalyse/0
compatible_end/0
is_3overhang/0
is_5overhang/0
is_blunt/0
overhang/0
Bio.Restriction.Restriction_Dictionary
Top
Bio.SCOP.Cla
Top
Summary
Functions
parse/0
Bio.SCOP.Cla.Index
Top
Summary
Functions
__getitem__/0
__init__/0
Bio.SCOP.Cla.Record
Top
Summary
Functions
__init__/0
Bio.SCOP.Des
Top
Summary
Functions
parse/0
Bio.SCOP.Des.Record
Top
Summary
Functions
__init__/0
_process/0
Bio.SCOP.Dom
Top
Summary
Functions
parse/0
Bio.SCOP.Dom.Record
Top
Summary
Functions
__init__/0
_process/0
Bio.SCOP.Hie
Top
Summary
Functions
parse/0
Bio.SCOP.Hie.Record
Top
Summary
Functions
__init__/0
_process/0
Bio.SCOP.Raf
Top
Summary
Functions
normalize_letters/0
parse/0
Bio.SCOP.Raf.Res
Top
Summary
Functions
__init__/0
Bio.SCOP.Raf.SeqMap
Top
Summary
Functions
__init__/0
_process/0
append/0
extend/0
getAtoms/0
Bio.SCOP.Raf.SeqMapIndex
Top
Summary
Functions
__getitem__/0
__init__/0
getSeqMap/0
Bio.SCOP.Residues
Top
Bio.SCOP.Residues.Residues
Top
Summary
Functions
__init__/0
Bio.SearchIO.BlatIO
Top
Summary
Functions
_list_from_csv/0
_reorient_starts/0
Bio.SearchIO.BlatIO.BlatPslIndexer
Top
Summary
Functions
__init__/0
__iter__/0
get_raw/0
Bio.SearchIO.BlatIO.BlatPslParser
Top
Summary
Functions
__init__/0
_parse_qresult/0
_parse_row/0
Bio.SearchIO.BlatIO.BlatPslWriter
Top
Summary
Functions
__init__/0
_build_row/0
Bio.SearchIO.FastaIO.FastaM10Indexer
Top
Summary
Functions
__init__/0
get_raw/0
Bio.SearchIO.FastaIO.FastaM10Parser
Top
Summary
Functions
__init__/0
__parse_hit_table/0
_parse_preamble/0
Bio.Seq
Top
Summary
Functions
_maketrans/0
_test/0
_translate_str/0
back_transcribe/0
complement/0
reverse_complement/0
transcribe/0
translate/0
Bio.Seq.MutableSeq
Top
Summary
Functions
__add__/0
__delitem__/0
__eq__/0
__getitem__/0
__init__/0
__le__/0
__len__/0
__lt__/0
__ne__/0
__radd__/0
__repr__/0
__setitem__/0
__str__/0
append/0
complement/0
count/0
count_overlap/0
extend/0
index/0
insert/0
pop/0
remove/0
reverse/0
reverse_complement/0
toseq/0
tostring/0
Bio.Seq.Seq
Top
Summary
Functions
__add__/0
__contains__/0
__eq__/0
__getitem__/0
__hash__/0
__init__/0
__le__/0
__len__/0
__lt__/0
__ne__/0
__radd__/0
__repr__/0
__str__/0
_get_seq_str_and_check_alphabet/0
back_transcribe/0
complement/0
count/0
count_overlap/0
endswith/0
find/0
lower/0
lstrip/0
reverse_complement/0
rfind/0
rsplit/0
rstrip/0
split/0
startswith/0
strip/0
tomutable/0
tostring/0
transcribe/0
translate/0
ungap/0
upper/0
Bio.Seq.UnknownSeq
Top
Summary
Functions
__add__/0
__getitem__/0
__init__/0
__len__/0
__radd__/0
__repr__/0
__str__/0
back_transcribe/0
complement/0
count/0
count_overlap/0
lower/0
reverse_complement/0
transcribe/0
translate/0
ungap/0
upper/0
Bio.SeqFeature
Top
Bio.SeqFeature.AbstractPosition
Top
Summary
Functions
__repr__/0
Bio.SeqFeature.AfterPosition
Top
Summary
Functions
__new__/0
__repr__/0
__str__/0
_flip/0
_shift/0
extension/0
position/0
Bio.SeqFeature.BeforePosition
Top
Summary
Functions
__new__/0
__repr__/0
__str__/0
_flip/0
_shift/0
extension/0
position/0
Bio.SeqFeature.BetweenPosition
Top
Summary
Functions
__new__/0
__repr__/0
__str__/0
_flip/0
_shift/0
extension/0
position/0
Bio.SeqFeature.ExactPosition
Top
Summary
Functions
__new__/0
__repr__/0
_flip/0
_shift/0
extension/0
position/0
Bio.SeqFeature.FeatureLocation
Top
Summary
Functions
__add__/0
__contains__/0
__eq__/0
__init__/0
__iter__/0
__len__/0
__ne__/0
__nonzero__/0
__radd__/0
__repr__/0
__str__/0
_flip/0
_get_strand/0
_set_strand/0
_shift/0
end/0
extract/0
nofuzzy_end/0
nofuzzy_start/0
parts/0
start/0
Bio.SeqFeature.OneOfPosition
Top
Summary
Functions
__new__/0
__repr__/0
__str__/0
_flip/0
_shift/0
extension/0
position/0
Bio.SeqFeature.PositionGap
Top
Summary
Functions
__init__/0
__repr__/0
__str__/0
Bio.SeqFeature.Reference
Top
Summary
Functions
__eq__/0
__init__/0
__ne__/0
__repr__/0
__str__/0
Bio.SeqFeature.UncertainPosition
Top
Bio.SeqFeature.UnknownPosition
Top
Summary
Functions
__hash__/0
__repr__/0
_flip/0
_shift/0
extension/0
position/0
Bio.SeqFeature.WithinPosition
Top
Summary
Functions
__new__/0
__repr__/0
__str__/0
_flip/0
_shift/0
extension/0
position/0
Bio.SeqIO.AbiIO
Top
Summary
Functions
AbiIterator/0
_AbiTrimIterator/0
_abi_parse_header/0
_abi_trim/0
_parse_tag_data/0
Bio.SeqIO.AceIO
Top
Summary
Functions
AceIterator/0
Bio.SeqIO.FastaIO
Top
Summary
Functions
FastaIterator/0
SimpleFastaParser/0
Bio.SeqIO.FastaIO.FastaWriter
Top
Summary
Functions
__init__/0
write_record/0
Bio.SeqIO.IgIO
Top
Summary
Functions
IgIterator/0
Bio.SeqIO.InsdcIO
Top
Summary
Functions
EmblCdsFeatureIterator/0
EmblIterator/0
GenBankCdsFeatureIterator/0
GenBankIterator/0
ImgtIterator/0
_insdc_feature_position_string/0
_insdc_location_string/0
Bio.SeqIO.InsdcIO.EmblWriter
Top
Summary
Functions
_write_the_first_lines/0
write_record/0
Bio.SeqIO.InsdcIO.GenBankWriter
Top
Summary
Functions
_get_topology/0
_write_multi_line/0
_write_single_line/0
_write_the_first_line/0
write_record/0
Bio.SeqIO.InsdcIO.ImgtWriter
Top
Bio.SeqIO.Interfaces
Top
Bio.SeqIO.Interfaces.SequenceIterator
Top
Summary
Functions
__init__/0
__iter__/0
__next__/0
next/0
Bio.SeqIO.Interfaces.SequenceWriter
Top
Summary
Functions
__init__/0
_get_seq_string/0
clean/0
write_file/0
Bio.SeqIO.Interfaces.SequentialSequenceWriter
Top
Summary
Functions
__init__/0
write_file/0
write_record/0
write_records/0
Bio.SeqIO.PdbIO
Top
Summary
Functions
PdbAtomIterator/0
PdbSeqresIterator/0
restype/0
Bio.SeqIO.PhdIO
Top
Summary
Functions
PhdIterator/0
Bio.SeqIO.PhdIO.PhdWriter
Top
Summary
Functions
__init__/0
write_record/0
Bio.SeqIO.PirIO
Top
Summary
Functions
PirIterator/0
Bio.SeqIO.PirIO.PirWriter
Top
Summary
Functions
__init__/0
write_record/0
Bio.SeqIO.QualityIO.FastqPhredWriter
Top
Summary
Functions
write_record/0
Bio.SeqIO.QualityIO.QualPhredWriter
Top
Summary
Functions
__init__/0
write_record/0
Bio.SeqIO.SeqXmlIO
Top
Bio.SeqIO.SeqXmlIO.SeqXmlIterator
Top
Summary
Functions
__init__/0
_attr_DBRef/0
_attr_entry/0
_attr_property/0
_attr_seqXML/0
_attr_species/0
_elem_AAseq/0
_elem_DNAseq/0
_elem_RNAseq/0
_elem_description/0
Bio.SeqIO.SeqXmlIO.SeqXmlWriter
Top
Summary
Functions
__init__/0
_write_dbxrefs/0
_write_description/0
_write_properties/0
_write_seq/0
_write_species/0
write_footer/0
write_header/0
write_record/0
Bio.SeqIO.SeqXmlIO.XMLRecordIterator
Top
Summary
Functions
__init__/0
__iter__/0
_attributes/0
Bio.SeqIO.SffIO
Top
Summary
Functions
ReadRocheXmlManifest/0
SffIterator/0
_SffTrimIterator/0
_check_eof/0
_check_mode/0
_get_read_region/0
_get_read_time/0
_get_read_xy/0
_sff_do_slow_index/0
_sff_file_header/0
_sff_find_roche_index/0
_sff_read_raw_record/0
_sff_read_roche_index/0
_sff_read_seq_record/0
_string_as_base_36/0
Bio.SeqIO.SffIO.SffWriter
Top
Summary
Functions
__init__/0
write_file/0
write_record/0
Bio.SeqIO.SwissIO
Top
Summary
Functions
SwissIterator/0
_make_position/0
_make_seqfeature/0
Bio.SeqIO.TabIO
Top
Summary
Functions
TabIterator/0
Bio.SeqIO.TabIO.TabWriter
Top
Summary
Functions
write_record/0
Bio.SeqIO.UniprotIO
Top
Summary
Functions
UniprotIterator/0
Bio.SeqIO.UniprotIO.Parser
Top
Summary
Functions
__init__/0
_parse_comment/0
_parse_protein/0
parse/0
Bio.SeqRecord
Top
Bio.SeqUtils.CheckSum
Top
Summary
Functions
crc32/0
crc64/0
gcg/0
seguid/0
Bio.SeqUtils.CodonUsage
Top
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex
Top
Summary
Functions
__init__/0
cai_for_gene/0
generate_index/0
print_index/0
set_cai_index/0
Bio.SeqUtils.CodonUsageIndices
Top
Bio.SeqUtils.IsoelectricPoint
Top
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint
Top
Summary
Functions
__init__/0
Bio.SeqUtils.MeltingTemp
Top
Summary
Functions
Tm_GC/0
Tm_NN/0
Tm_Wallace/0
Tm_staluc/0
_check/0
_key_error/0
chem_correction/0
make_table/0
salt_correction/0
Bio.SeqUtils.ProtParam
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Bio.SeqUtils.ProtParam.ProteinAnalysis
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Summary
Functions
__init__/0
_weight_list/0
aromaticity/0
count_amino_acids/0
flexibility/0
get_amino_acids_percent/0
gravy/0
instability_index/0
isoelectric_point/0
molar_extinction_coefficient/0
molecular_weight/0
protein_scale/0
secondary_structure_fraction/0
Bio.SeqUtils.ProtParamData
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Bio.Sequencing.Ace.ACEFileRecord
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Summary
Functions
__init__/0
sort/0
Bio.Sequencing.Ace.Reads
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Summary
Functions
__init__/0
Bio.Sequencing.Phd
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Summary
Functions
parse/0
read/0
Bio.Sequencing.Phd.Record
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Summary
Functions
__init__/0
Bio.SubsMat.FreqTable
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Bio.SubsMat.FreqTable.FreqTable
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Summary
Functions
__init__/0
Bio.SubsMat.MatrixInfo
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Bio.SwissProt.KeyWList
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Bio.SwissProt.KeyWList.Record
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Summary
Functions
__init__/0
Bio.UniProt.GOA
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Summary
Functions
_gpa10iterator/0
_gpa11iterator/0
_gpi10iterator/0
_gpi11iterator/0
gafbyproteiniterator/0
gafiterator/0
gpa_iterator/0
gpi_iterator/0
record_has/0
writebyproteinrec/0
writerec/0
Biopython
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biopython v1.71.0
Bio.PDB.Chain
Chain class, used in Structure objects.