biopython

v1.71.0

biopython v1.71.0 Bio.Phylo.PhyloXML.Phylogeny

A phylogenetic tree.

:Parameters:

root : Clade
    the root node/clade of this tree
rooted : bool
    True if this tree is rooted
rerootable : bool
    True if this tree is rerootable
branch_length_unit : string
    unit for branch_length values on clades
name : string
    identifier for this tree, not required to be unique
id : Id
    unique identifier for this tree
description : string
    plain-text description
date : Date
    date for the root node of this tree
confidences : list
    Confidence objects for this tree
clade_relations : list
    CladeRelation objects
sequence_relations : list
    SequenceRelation objects
properties : list
    Property objects
other : list
    non-phyloXML elements (type `Other`)

Link to this section Summary

Functions

__init__()

Initialize values for phylogenetic tree object

_get_confidence()

Equivalent to self.confidences[0] if there is only 1 value

as_phyloxml()

Return this tree, a PhyloXML-compatible Phylogeny object

from_clade()

Create a new Phylogeny given a Newick or BaseTree Clade object

from_tree()

Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree)

to_alignment()

Construct an alignment from the aligned sequences in this tree

to_phyloxml_container()

Create a new Phyloxml object containing just this phylogeny

Link to this section Functions

Link to this function __init__()

Initialize values for phylogenetic tree object.

Link to this function _get_confidence()

Equivalent to self.confidences[0] if there is only 1 value.

See Also: Clade.confidence, Clade.taxonomy

Link to this function as_phyloxml()

Return this tree, a PhyloXML-compatible Phylogeny object.

Overrides the BaseTree method.

Link to this function from_clade()

Create a new Phylogeny given a Newick or BaseTree Clade object.

Keyword arguments are the usual PhyloXML.Clade constructor parameters.

Link to this function from_tree()

Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree).

Keyword arguments are the usual Phylogeny constructor parameters.

Link to this function to_alignment()

Construct an alignment from the aligned sequences in this tree.

Link to this function to_phyloxml_container()

Create a new Phyloxml object containing just this phylogeny.