Bio.Phylo package

Subpackages

• Bio.Phylo.PAML package
  • Submodules
    • Bio.Phylo.PAML.baseml module
      • BasemlError
      • Baseml
      • read()
    • Bio.Phylo.PAML.chi2 module
      • cdf_chi2()
    • Bio.Phylo.PAML.codeml module
      • CodemlError
      • Codeml
      • read()
    • Bio.Phylo.PAML.yn00 module
      • Yn00Error
      • Yn00
      • read()
  • Module contents

Submodules

• Bio.Phylo.BaseTree module
  • 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__()
    • Tree.__annotations__
  • Clade
    • Clade.__init__()
    • Clade.root
    • Clade.is_terminal()
    • Clade.__getitem__()
    • Clade.__iter__()
    • Clade.__len__()
    • Clade.__bool__()
    • Clade.__str__()
    • Clade.color
    • Clade.__annotations__
  • 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 module
  • Tree
    • Tree.__init__()
    • Tree.__annotations__
  • Clade
    • Clade.__init__()
    • Clade.__annotations__
• Bio.Phylo.CDAOIO module
  • 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 module
  • strict_consensus()
  • majority_consensus()
  • adam_consensus()
  • get_support()
  • bootstrap()
  • bootstrap_trees()
  • bootstrap_consensus()
• Bio.Phylo.NeXML module
  • Tree
    • Tree.__init__()
    • Tree.__annotations__
  • Clade
    • Clade.__init__()
    • Clade.__annotations__
• Bio.Phylo.NeXMLIO module
  • 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 module
  • Tree
    • Tree.__init__()
    • Tree.__annotations__
  • Clade
    • Clade.__init__()
    • Clade.__annotations__
• Bio.Phylo.NewickIO module
  • 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 module
  • parse()
  • write()
• Bio.Phylo.PhyloXML module
  • See Also
  • PhyloXMLWarning
    • PhyloXMLWarning.__annotations__
  • PhyloElement
    • PhyloElement.__annotations__
  • Phyloxml
    • Phyloxml.__init__()
    • Phyloxml.__getitem__()
    • Phyloxml.__iter__()
    • Phyloxml.__len__()
    • Phyloxml.__str__()
    • Phyloxml.__annotations__
  • Other
    • Other.__init__()
    • Other.__iter__()
    • Other.__annotations__
  • Phylogeny
    • Phylogeny.__init__()
    • Phylogeny.from_tree()
    • Phylogeny.from_clade()
    • Phylogeny.as_phyloxml()
    • Phylogeny.to_phyloxml_container()
    • Phylogeny.to_alignment()
    • Phylogeny.alignment
    • Phylogeny.confidence
    • Phylogeny.__annotations__
  • Clade
    • Clade.__init__()
    • Clade.from_clade()
    • Clade.to_phylogeny()
    • Clade.confidence
    • Clade.taxonomy
    • Clade.__annotations__
  • BranchColor
    • BranchColor.__init__()
    • BranchColor.__annotations__
  • Accession
    • Accession.__init__()
    • Accession.__str__()
    • Accession.__annotations__
  • Annotation
    • Annotation.re_ref
    • Annotation.__init__()
    • Annotation.__annotations__
  • BinaryCharacters
    • BinaryCharacters.__init__()
    • BinaryCharacters.__annotations__
  • CladeRelation
    • CladeRelation.__init__()
    • CladeRelation.__annotations__
  • Confidence
    • Confidence.__new__()
    • Confidence.value
    • Confidence.__annotations__
  • Date
    • Date.__init__()
    • Date.__str__()
    • Date.__annotations__
  • Distribution
    • Distribution.__init__()
    • Distribution.__annotations__
  • DomainArchitecture
    • DomainArchitecture.__init__()
    • DomainArchitecture.__annotations__
  • Events
    • Events.ok_type
    • Events.__init__()
    • Events.items()
    • Events.keys()
    • Events.values()
    • Events.__len__()
    • Events.__getitem__()
    • Events.__setitem__()
    • Events.__delitem__()
    • Events.__iter__()
    • Events.__contains__()
    • Events.__annotations__
  • Id
    • Id.__init__()
    • Id.__str__()
    • Id.__annotations__
  • MolSeq
    • MolSeq.re_value
    • MolSeq.__init__()
    • MolSeq.__str__()
    • MolSeq.__annotations__
  • Point
    • Point.__init__()
    • Point.__annotations__
  • Polygon
    • Polygon.__init__()
    • Polygon.__str__()
    • Polygon.__annotations__
  • Property
    • Property.re_ref
    • Property.ok_applies_to
    • Property.ok_datatype
    • Property.__init__()
    • Property.__annotations__
  • ProteinDomain
    • ProteinDomain.__init__()
    • ProteinDomain.from_seqfeature()
    • ProteinDomain.to_seqfeature()
    • ProteinDomain.__annotations__
  • Reference
    • Reference.re_doi
    • Reference.__init__()
    • Reference.__annotations__
  • Sequence
    • Sequence.types
    • Sequence.re_symbol
    • Sequence.__init__()
    • Sequence.from_seqrecord()
    • Sequence.to_seqrecord()
    • Sequence.__annotations__
  • SequenceRelation
    • SequenceRelation.ok_type
    • SequenceRelation.__init__()
    • SequenceRelation.__annotations__
  • Taxonomy
    • Taxonomy.re_code
    • Taxonomy.ok_rank
    • Taxonomy.__init__()
    • Taxonomy.__str__()
    • Taxonomy.__annotations__
  • Uri
    • Uri.__init__()
    • Uri.__str__()
    • Uri.__annotations__
• Bio.Phylo.PhyloXMLIO module
  • 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 module
  • DistanceMatrix
    • DistanceMatrix.__init__()
    • DistanceMatrix.__setitem__()
    • DistanceMatrix.format_phylip()
  • DistanceCalculator
    • DistanceCalculator.dna_models
    • DistanceCalculator.protein_models
    • DistanceCalculator.models
    • DistanceCalculator.__init__()
    • DistanceCalculator.get_distance()
  • TreeConstructor
    • TreeConstructor.build_tree()
  • DistanceTreeConstructor
    • DistanceTreeConstructor.methods
    • DistanceTreeConstructor.__init__()
    • DistanceTreeConstructor.build_tree()
    • DistanceTreeConstructor.upgma()
    • DistanceTreeConstructor.nj()
    • DistanceTreeConstructor.__annotations__
  • Scorer
    • Scorer.get_score()
  • TreeSearcher
    • TreeSearcher.search()
  • NNITreeSearcher
    • NNITreeSearcher.__init__()
    • NNITreeSearcher.search()
    • NNITreeSearcher.__annotations__
  • ParsimonyScorer
    • ParsimonyScorer.__init__()
    • ParsimonyScorer.get_score()
    • ParsimonyScorer.__annotations__
  • ParsimonyTreeConstructor
    • ParsimonyTreeConstructor.__annotations__
    • ParsimonyTreeConstructor.__init__()
    • ParsimonyTreeConstructor.build_tree()

Module contents

Package for working with phylogenetic trees.

See Also: http://biopython.org/wiki/Phylo