Bio.Phylo 套件

子套件

• Bio.Phylo.Applications 套件
  • 模組內容
    • PhymlCommandline
      • PhymlCommandline.__init__()
      • PhymlCommandline.alpha
      • PhymlCommandline.bootstrap
      • PhymlCommandline.datatype
      • PhymlCommandline.frequencies
      • PhymlCommandline.input
      • PhymlCommandline.input_tree
      • PhymlCommandline.model
      • PhymlCommandline.multiple
      • PhymlCommandline.n_rand_starts
      • PhymlCommandline.nclasses
      • PhymlCommandline.optimize
      • PhymlCommandline.pars
      • PhymlCommandline.print_site_lnl
      • PhymlCommandline.print_trace
      • PhymlCommandline.prop_invar
      • PhymlCommandline.quiet
      • PhymlCommandline.r_seed
      • PhymlCommandline.rand_start
      • PhymlCommandline.run_id
      • PhymlCommandline.search
      • PhymlCommandline.sequential
      • PhymlCommandline.ts_tv_ratio
    • RaxmlCommandline
      • RaxmlCommandline.__init__()
      • RaxmlCommandline.parsimony_seed
      • RaxmlCommandline.algorithm
      • RaxmlCommandline.binary_constraint
      • RaxmlCommandline.bipartition_filename
      • RaxmlCommandline.bootstrap_branch_lengths
      • RaxmlCommandline.bootstrap_seed
      • RaxmlCommandline.checkpoints
      • RaxmlCommandline.cluster_threshold
      • RaxmlCommandline.cluster_threshold_fast
      • RaxmlCommandline.epsilon
      • RaxmlCommandline.exclude_filename
      • RaxmlCommandline.grouping_constraint
      • RaxmlCommandline.model
      • RaxmlCommandline.name
      • RaxmlCommandline.num_bootstrap_searches
      • RaxmlCommandline.num_categories
      • RaxmlCommandline.num_replicates
      • RaxmlCommandline.outgroup
      • RaxmlCommandline.parsimony
      • RaxmlCommandline.partition_branch_lengths
      • RaxmlCommandline.partition_filename
      • RaxmlCommandline.protein_model
      • RaxmlCommandline.random_starting_tree
      • RaxmlCommandline.rapid_bootstrap_seed
      • RaxmlCommandline.rearrangements
      • RaxmlCommandline.sequences
      • RaxmlCommandline.starting_tree
      • RaxmlCommandline.threads
      • RaxmlCommandline.version
      • RaxmlCommandline.weight_filename
      • RaxmlCommandline.working_dir
    • FastTreeCommandline
      • FastTreeCommandline.__init__()
      • FastTreeCommandline.bionj
      • FastTreeCommandline.boot
      • FastTreeCommandline.cat
      • FastTreeCommandline.close
      • FastTreeCommandline.constraintWeight
      • FastTreeCommandline.constraints
      • FastTreeCommandline.expert
      • FastTreeCommandline.fastest
      • FastTreeCommandline.gamma
      • FastTreeCommandline.gtr
      • FastTreeCommandline.gtrfreq
      • FastTreeCommandline.gtrrates
      • FastTreeCommandline.help
      • FastTreeCommandline.input
      • FastTreeCommandline.intree
      • FastTreeCommandline.intree1
      • FastTreeCommandline.log
      • FastTreeCommandline.makematrix
      • FastTreeCommandline.matrix
      • FastTreeCommandline.mlacc
      • FastTreeCommandline.mllen
      • FastTreeCommandline.mlnni
      • FastTreeCommandline.n
      • FastTreeCommandline.nj
      • FastTreeCommandline.nni
      • FastTreeCommandline.no2nd
      • FastTreeCommandline.nocat
      • FastTreeCommandline.nomatrix
      • FastTreeCommandline.nome
      • FastTreeCommandline.noml
      • FastTreeCommandline.nopr
      • FastTreeCommandline.nosupport
      • FastTreeCommandline.notop
      • FastTreeCommandline.nt
      • FastTreeCommandline.out
      • FastTreeCommandline.pseudo
      • FastTreeCommandline.quiet
      • FastTreeCommandline.quote
      • FastTreeCommandline.rawdist
      • FastTreeCommandline.refresh
      • FastTreeCommandline.second
      • FastTreeCommandline.seed
      • FastTreeCommandline.slow
      • FastTreeCommandline.slownni
      • FastTreeCommandline.spr
      • FastTreeCommandline.sprlength
      • FastTreeCommandline.top
      • FastTreeCommandline.topm
      • FastTreeCommandline.wag
• Bio.Phylo.PAML 套件
  • 子模組
    • Bio.Phylo.PAML.baseml 模組
      • BasemlError
      • Baseml
      • read()
    • Bio.Phylo.PAML.chi2 模組
      • cdf_chi2()
    • Bio.Phylo.PAML.codeml 模組
      • CodemlError
      • Codeml
      • read()
    • Bio.Phylo.PAML.yn00 模組
      • Yn00Error
      • Yn00
      • read()
  • 模組內容

子模組

• Bio.Phylo.BaseTree 模組
  • TreeElement
    • TreeElement.__repr__()
    • TreeElement.__str__()
  • TreeMixin
    • TreeMixin.find_any()
    • TreeMixin.find_elements()
    • TreeMixin.find_clades()
    • TreeMixin.get_path()
    • TreeMixin.get_nonterminals()
    • TreeMixin.get_terminals()
    • TreeMixin.trace()
    • TreeMixin.common_ancestor()
    • TreeMixin.count_terminals()
    • TreeMixin.depths()
    • TreeMixin.distance()
    • TreeMixin.is_bifurcating()
    • TreeMixin.is_monophyletic()
    • TreeMixin.is_parent_of()
    • TreeMixin.is_preterminal()
    • TreeMixin.total_branch_length()
    • TreeMixin.collapse()
    • TreeMixin.collapse_all()
    • TreeMixin.ladderize()
    • TreeMixin.prune()
    • TreeMixin.split()
  • Tree
    • Tree.__init__()
    • Tree.from_clade()
    • Tree.randomized()
    • Tree.clade
    • Tree.as_phyloxml()
    • Tree.root_with_outgroup()
    • Tree.root_at_midpoint()
    • Tree.is_terminal()
    • Tree.__format__()
    • Tree.format()
    • Tree.__str__()
  • Clade
    • Clade.__init__()
    • Clade.root
    • Clade.is_terminal()
    • Clade.__getitem__()
    • Clade.__iter__()
    • Clade.__len__()
    • Clade.__bool__()
    • Clade.__str__()
    • Clade.color
  • BranchColor
    • BranchColor.color_names
    • BranchColor.__init__()
    • BranchColor.from_hex()
    • BranchColor.from_name()
    • BranchColor.to_hex()
    • BranchColor.to_rgb()
    • BranchColor.__repr__()
    • BranchColor.__str__()
• Bio.Phylo.CDAO 模組
  • Tree
    • Tree.__init__()
  • Clade
    • Clade.__init__()
• Bio.Phylo.CDAOIO 模組
  • qUri()
  • format_label()
  • parse()
  • write()
  • Parser
    • Parser.__init__()
    • Parser.from_string()
    • Parser.parse()
    • Parser.parse_handle_to_graph()
    • Parser.parse_graph()
    • Parser.new_clade()
    • Parser.get_node_info()
    • Parser.parse_children()
  • Writer
    • Writer.prefixes
    • Writer.__init__()
    • Writer.write()
    • Writer.add_stmt_to_handle()
    • Writer.process_clade()
• Bio.Phylo.Consensus 模組
  • strict_consensus()
  • majority_consensus()
  • adam_consensus()
  • get_support()
  • bootstrap()
  • bootstrap_trees()
  • bootstrap_consensus()
• Bio.Phylo.NeXML 模組
  • Tree
    • Tree.__init__()
  • Clade
    • Clade.__init__()
• Bio.Phylo.NeXMLIO 模組
  • qUri()
  • cdao_to_obo()
  • matches()
  • NeXMLError
  • parse()
  • write()
  • Parser
    • Parser.__init__()
    • Parser.from_string()
    • Parser.add_annotation()
    • Parser.parse()
  • Writer
    • Writer.__init__()
    • Writer.new_label()
    • Writer.write()
• Bio.Phylo.Newick 模組
  • Tree
    • Tree.__init__()
  • Clade
    • Clade.__init__()
• Bio.Phylo.NewickIO 模組
  • NewickError
  • parse()
  • write()
  • Parser
    • Parser.__init__()
    • Parser.from_string()
    • Parser.parse()
    • Parser.new_clade()
    • Parser.process_clade()
  • Writer
    • Writer.__init__()
    • Writer.write()
    • Writer.to_strings()
• Bio.Phylo.NexusIO 模組
  • parse()
  • write()
• Bio.Phylo.PhyloXML 模組
  • 另請參閱
  • PhyloXMLWarning
  • PhyloElement
  • Phyloxml
    • Phyloxml.__init__()
    • Phyloxml.__getitem__()
    • Phyloxml.__iter__()
    • Phyloxml.__len__()
    • Phyloxml.__str__()
  • Other
    • Other.__init__()
    • Other.__iter__()
  • Phylogeny
    • Phylogeny.__init__()
    • Phylogeny.from_tree()
    • Phylogeny.from_clade()
    • Phylogeny.as_phyloxml()
    • Phylogeny.to_phyloxml_container()
    • Phylogeny.to_alignment()
    • Phylogeny.alignment
    • Phylogeny.confidence
  • Clade
    • Clade.__init__()
    • Clade.from_clade()
    • Clade.to_phylogeny()
    • Clade.confidence
    • Clade.taxonomy
  • BranchColor
    • BranchColor.__init__()
  • Accession
    • Accession.__init__()
    • Accession.__str__()
  • Annotation
    • Annotation.re_ref
    • Annotation.__init__()
  • BinaryCharacters
    • BinaryCharacters.__init__()
  • CladeRelation
    • CladeRelation.__init__()
  • Confidence
    • Confidence.__new__()
    • Confidence.value
  • Date
    • Date.__init__()
    • Date.__str__()
  • Distribution
    • Distribution.__init__()
  • DomainArchitecture
    • DomainArchitecture.__init__()
  • Events
    • Events.ok_type
    • Events.__init__()
    • Events.items()
    • Events.keys()
    • Events.values()
    • Events.__len__()
    • Events.__getitem__()
    • Events.__setitem__()
    • Events.__delitem__()
    • Events.__iter__()
    • Events.__contains__()
  • Id
    • Id.__init__()
    • Id.__str__()
  • MolSeq
    • MolSeq.re_value
    • MolSeq.__init__()
    • MolSeq.__str__()
  • Point
    • Point.__init__()
  • Polygon
    • Polygon.__init__()
    • Polygon.__str__()
  • Property
    • Property.re_ref
    • Property.ok_applies_to
    • Property.ok_datatype
    • Property.__init__()
  • ProteinDomain
    • ProteinDomain.__init__()
    • ProteinDomain.from_seqfeature()
    • ProteinDomain.to_seqfeature()
  • Reference
    • Reference.re_doi
    • Reference.__init__()
  • Sequence
    • Sequence.types
    • Sequence.re_symbol
    • Sequence.__init__()
    • Sequence.from_seqrecord()
    • Sequence.to_seqrecord()
  • SequenceRelation
    • SequenceRelation.ok_type
    • SequenceRelation.__init__()
  • Taxonomy
    • Taxonomy.re_code
    • Taxonomy.ok_rank
    • Taxonomy.__init__()
    • Taxonomy.__str__()
  • Uri
    • Uri.__init__()
    • Uri.__str__()
• Bio.Phylo.PhyloXMLIO 模組
  • PhyloXMLError
  • read()
  • parse()
  • write()
  • Parser
    • Parser.__init__()
    • Parser.read()
    • Parser.parse()
    • Parser.other()
    • Parser.accession()
    • Parser.annotation()
    • Parser.binary_characters()
    • Parser.clade_relation()
    • Parser.color()
    • Parser.confidence()
    • Parser.date()
    • Parser.distribution()
    • Parser.domain()
    • Parser.domain_architecture()
    • Parser.events()
    • Parser.id()
    • Parser.mol_seq()
    • Parser.point()
    • Parser.polygon()
    • Parser.property()
    • Parser.reference()
    • Parser.sequence_relation()
    • Parser.uri()
  • Writer
    • Writer.__init__()
    • Writer.write()
    • Writer.phyloxml()
    • Writer.other()
    • Writer.phylogeny()
    • Writer.clade()
    • Writer.accession()
    • Writer.annotation()
    • Writer.binary_characters()
    • Writer.clade_relation()
    • Writer.color()
    • Writer.confidence()
    • Writer.date()
    • Writer.distribution()
    • Writer.domain()
    • Writer.domain_architecture()
    • Writer.events()
    • Writer.id()
    • Writer.mol_seq()
    • Writer.node_id()
    • Writer.point()
    • Writer.polygon()
    • Writer.property()
    • Writer.reference()
    • Writer.sequence()
    • Writer.sequence_relation()
    • Writer.taxonomy()
    • Writer.uri()
    • Writer.alt()
    • Writer.branch_length()
    • Writer.lat()
    • Writer.long()
    • Writer.maximum()
    • Writer.minimum()
    • Writer.value()
    • Writer.width()
    • Writer.blue()
    • Writer.duplications()
    • Writer.green()
    • Writer.losses()
    • Writer.red()
    • Writer.speciations()
    • Writer.bc()
    • Writer.code()
    • Writer.common_name()
    • Writer.desc()
    • Writer.description()
    • Writer.location()
    • Writer.name()
    • Writer.rank()
    • Writer.scientific_name()
    • Writer.symbol()
    • Writer.synonym()
    • Writer.type()
• Bio.Phylo.TreeConstruction 模組
  • DistanceMatrix (距離矩陣)
    • DistanceMatrix.__init__()
    • DistanceMatrix.__setitem__()
    • DistanceMatrix.format_phylip()
  • DistanceCalculator (距離計算器)
    • DistanceCalculator.dna_models (DNA 模型)
    • DistanceCalculator.protein_models (蛋白質模型)
    • DistanceCalculator.models (模型)
    • DistanceCalculator.__init__()
    • DistanceCalculator.get_distance()
  • TreeConstructor (樹狀建構器)
    • TreeConstructor.build_tree()
  • DistanceTreeConstructor (距離樹狀建構器)
    • DistanceTreeConstructor.methods (方法)
    • DistanceTreeConstructor.__init__()
    • DistanceTreeConstructor.build_tree()
    • DistanceTreeConstructor.upgma()
    • DistanceTreeConstructor.nj()
  • Scorer (評分器)
    • Scorer.get_score()
  • TreeSearcher (樹狀搜尋器)
    • TreeSearcher.search()
  • NNITreeSearcher (最近鄰居交換樹狀搜尋器)
    • NNITreeSearcher.__init__()
    • NNITreeSearcher.search()
  • ParsimonyScorer (最大簡約評分器)
    • ParsimonyScorer.__init__()
    • ParsimonyScorer.get_score()
  • ParsimonyTreeConstructor (最大簡約樹狀建構器)
    • ParsimonyTreeConstructor.__init__()
    • ParsimonyTreeConstructor.build_tree()

模組內容

用於處理親緣關係樹的套件。

另請參閱: https://biopython.dev.org.tw/wiki/Phylo