biopython v1.71.0 Bio.Phylo.PhyloXML.Clade
Describes a branch of the current phylogenetic tree.
Used recursively, describes the topology of a phylogenetic tree.
Both color
and width
elements should be interpreted by client code
as applying to the whole clade, including all descendents, unless
overwritten in-sub clades. This module doesn’t automatically assign these
attributes to sub-clades to achieve this cascade — and neither should you.
:Parameters:
branch_length
parent branch length of this clade
id_source
link other elements to a clade (on the xml-level)
name : string
short label for this clade
confidences : list of Confidence objects
used to indicate the support for a clade/parent branch.
width : float
branch width for this clade (including branch from parent)
color : BranchColor
color used for graphical display of this clade
node_id
unique identifier for the root node of this clade
taxonomies : list
Taxonomy objects
sequences : list
Sequence objects
events : Events
describe such events as gene-duplications at the root node/parent
branch of this clade
binary_characters : BinaryCharacters
binary characters
distributions : list of Distribution objects
distribution(s) of this clade
date : Date
a date for the root node of this clade
references : list
Reference objects
properties : list
Property objects
clades : list Clade objects
Sub-clades
other : list of Other objects
non-phyloXML objects
Link to this section Summary
Functions
Initialize value for the Clade object
Create a new PhyloXML Clade from a Newick or BaseTree Clade object
Create a new phylogeny containing just this clade
Link to this section Functions
Initialize value for the Clade object.
Create a new PhyloXML Clade from a Newick or BaseTree Clade object.
Keyword arguments are the usual PhyloXML Clade constructor parameters.
Create a new phylogeny containing just this clade.