PhyloTree class

class PhyloNode(newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x25629b0>, format=0)

Bases: ete2.coretype.tree.TreeNode

Extends the standard TreeNode instance. It adds specific attributes and methods to work with phylogentic trees.

Parameters:
  • newick – Path to the file containing the tree or, alternatively, the text string containing the same information.
  • alignment – file containing a multiple sequence alignment.
  • alg_format – “fasta”, “phylip” or “iphylip” (interleaved)
  • format

    sub-newick format

    FORMAT DESCRIPTION
    0 flexible with support values
    1 flexible with internal node names
    2 all branches + leaf names + internal supports
    3 all branches + all names
    4 leaf branches + leaf names
    5 internal and leaf branches + leaf names
    6 internal branches + leaf names
    7 leaf branches + all names
    8 all names
    9 leaf names
    100 topology only
  • sp_naming_function – Pointer to a parsing python function that receives nodename as first argument and returns the species name (see PhyloNode.set_species_naming_function(). By default, the 3 first letter of nodes will be used as species identifiers.
Returns:

a tree node object which represents the base of the tree.

get_age(species2age)
get_age_balanced_outgroup(species2age)

New in version 2.x.

Returns the best outgroup according to topological ages and node sizes.

Currently Experimental !!

get_descendant_evol_events(sos_thr=0.0)

Returns a list of all duplication and speciation events detected after this node. Nodes are assumed to be duplications when a species overlap is found between its child linages. Method is described more detail in:

“The Human Phylome.” Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon T. Genome Biol. 2007;8(6):R109.

get_farthest_oldest_leaf(species2age, is_leaf_fn=None)

Returns the farthest oldest leaf to the current one. It requires an species2age dictionary with the age estimation for all species.

Parameters:is_leaf_fn (None) – A pointer to a function that receives a node instance as unique argument and returns True or False. It can be used to dynamically collapse nodes, so they are seen as leaves.
get_farthest_oldest_node(species2age)

New in version 2.1.

Returns the farthest oldest node (leaf or internal). The difference with get_farthest_oldest_leaf() is that in this function internal nodes grouping seqs from the same species are collapsed.

get_my_evol_events(sos_thr=0.0)

Returns a list of duplication and speciation events in which the current node has been involved. Scanned nodes are also labeled internally as dup=True|False. You can access this labels using the ‘node.dup’ sintaxis.

Method: the algorithm scans all nodes from the given leafName to the root. Nodes are assumed to be duplications when a species overlap is found between its child linages. Method is described more detail in:

“The Human Phylome.” Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon T. Genome Biol. 2007;8(6):R109.

get_species()

Returns the set of species covered by its partition.

is_monophyletic(species)

Returns True id species names under this node are all included in a given list or set of species names.

iter_species()

Returns an iterator over the species grouped by this node.

reconcile(species_tree)

Returns the reconcilied topology with the provided species tree, and a list of evolutionary events inferred from such reconciliation.

set_species_naming_function(fn)

Sets the parsing function used to extract species name from a node’s name.

Parameters:fn – Pointer to a parsing python function that receives nodename as first argument and returns the species name.
# Example of a parsing function to extract species names for
# all nodes in a given tree.
def parse_sp_name(node_name):
    return node_name.split("_")[1]
tree.set_species_naming_function(parse_sp_name)
species
PhyloTree

alias of PhyloNode

class EvolEvent

Basic evolutionary event. It stores all the information about an event(node) ocurred in a phylogenetic tree.

etype : D (Duplication), S (Speciation), L (gene loss),

in_seqs : the list of sequences in one side of the event.

out_seqs : the list of sequences in the other side of the event

node : link to the event node in the tree

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