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.