Bio.Phylo package
Subpackages
Submodules
- Bio.Phylo.BaseTree module
TreeElementTreeMixinTreeMixin.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()TreeMixin.__annotate_func__TreeMixin.__annotations_cache__TreeMixin.__firstlineno__TreeMixin.__static_attributes__
TreeCladeBranchColorBranchColor.color_namesBranchColor.__init__()BranchColor.from_hex()BranchColor.from_name()BranchColor.to_hex()BranchColor.to_rgb()BranchColor.__repr__()BranchColor.__annotate_func__BranchColor.__annotations_cache__BranchColor.__firstlineno__BranchColor.__static_attributes__BranchColor.__str__()
- Bio.Phylo.CDAO module
- Bio.Phylo.CDAOIO module
- Bio.Phylo.Consensus module
- Bio.Phylo.NeXML module
- Bio.Phylo.NeXMLIO module
- Bio.Phylo.Newick module
- Bio.Phylo.NewickIO module
- Bio.Phylo.NexusIO module
- Bio.Phylo.PhyloXML module
- See Also
PhyloXMLWarningPhyloElementPhyloxmlOtherPhylogenyPhylogeny.__init__()Phylogeny.from_tree()Phylogeny.from_clade()Phylogeny.as_phyloxml()Phylogeny.to_phyloxml_container()Phylogeny.to_alignment()Phylogeny.alignmentPhylogeny.confidencePhylogeny.__annotate_func__Phylogeny.__annotations_cache__Phylogeny.__firstlineno__Phylogeny.__static_attributes__
CladeBranchColorAccessionAnnotationBinaryCharactersCladeRelationConfidenceDateDistributionDomainArchitectureEventsEvents.ok_typeEvents.__init__()Events.items()Events.keys()Events.values()Events.__len__()Events.__getitem__()Events.__setitem__()Events.__delitem__()Events.__iter__()Events.__contains__()Events.__annotate_func__Events.__annotations_cache__Events.__firstlineno__Events.__static_attributes__
IdMolSeqPointPolygonPropertyProteinDomainReferenceSequenceSequenceRelationTaxonomyUri
- Bio.Phylo.PhyloXMLIO module
PhyloXMLErrorread()parse()write()ParserParser.__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()Parser.__annotate_func__Parser.__annotations_cache__Parser.__firstlineno__Parser.__static_attributes__
WriterWriter.__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()Writer.__annotate_func__Writer.__annotations_cache__Writer.__firstlineno__Writer.__static_attributes__
- Bio.Phylo.TreeConstruction module
DistanceMatrixDistanceCalculatorDistanceCalculator.dna_modelsDistanceCalculator.protein_modelsDistanceCalculator.modelsDistanceCalculator.__init__()DistanceCalculator.get_distance()DistanceCalculator.__annotate_func__DistanceCalculator.__annotations_cache__DistanceCalculator.__firstlineno__DistanceCalculator.__static_attributes__
TreeConstructorDistanceTreeConstructorDistanceTreeConstructor.methodsDistanceTreeConstructor.__init__()DistanceTreeConstructor.build_tree()DistanceTreeConstructor.upgma()DistanceTreeConstructor.nj()DistanceTreeConstructor.__annotate_func__DistanceTreeConstructor.__annotations_cache__DistanceTreeConstructor.__firstlineno__DistanceTreeConstructor.__static_attributes__
ScorerTreeSearcherNNITreeSearcherParsimonyScorerParsimonyTreeConstructor
Module contents
Package for working with phylogenetic trees.
See Also: http://biopython.org/wiki/Phylo