mrnoutahi Some thoughts on boring stuff, and bioinformatics

Why you should use ete for tree exploration and visualisation in python !

If you work with trees (phylogenetics or not) and you regularly use python, you have probably used or heard about one of the following packages: Bio.phylo, dendropy or ETE.

While each one of those packages has its own unique strengths and weaknesses, I particularly like the ETE module. Here is why !

This post is based on one of my past presentation at monbug. I actually convert the ipython notebook to this markdown with nbconvert as described by Christopher S. Corley on his blog. The config I used with nbconvert can be found here. The github repository with all the original files for the presentation can be found here : monbug_ete. You can use nbviewer to view the notebook directly if you prefer.

What’s ETE ??

ETE is a python Environment for Tree Exploration created by Jaime Huerta-Cepas.

It’s a framework that assists in the manipulation of any type of hierarchical tree (ie reading, writing, visualisation, annotation, etc). The current latest version is ete3.


You can install ETE with pip : pip install ete3. Check this link for more details about optional/unmet dependencies :

Quick introduction to the API

A great in-depth tutorial for working with tree data structure in ETE is provided by the authors : I’m going to make a light introduction to the API here, but I really recommend you to read the official doc!

Let’s take a quick glance at the available tree data structure in ete :

In [58]:

import ete3
import inspect
print([x[0] for x in inspect.getmembers(ete3, inspect.isclass) if x[0].endswith('Tree')])
['ClusterTree', 'EvolTree', 'NexmlTree', 'PhyloTree', 'PhyloxmlTree', 'Tree']

As you can see, you have a basic tree data structure (Tree) and more specialized tree structures, like PhyloTree for phylogenetics

=> ETE can read tree from a string or a file

In [59]:

from ete3 import Tree

rand_newick = "((((a,b), c), d), (e,f));"
rand_tree = "rand_tree"
with open(rand_tree, 'w') as TREE:

# Reading tree t1 and t2
t1 = Tree(rand_newick)
t2 = Tree(rand_tree)

=> In ete, a tree is a Node. This implies that the root is a Node, so are all its descendants.

In [61]:

      /-|   \-b
     |  |
   /-|   \-c
  |  |
--|   \-d
  |   /-e

=> You can add information to nodes by adding features

The following code will traverse the tree t1 and add a feature sexiness to each leaf.

In [62]:

from numpy import random

# Traverse : levelorder, preorder, postorder
for node in t1.traverse("levelorder"):
    if node.is_leaf():
        # add a features : randomness
        node_rand = random.randint(10)

=> Features are just attributes.

In [63]:

# print t1 again with features : name and sexiness
print(t1.get_ascii(attributes=['name', 'sexiness']))
            /-a, 8
      /-|   \-b, 1
     |  |
   /-|   \-c, 9
  |  |
--|   \-d, 3
  |   /-e, 9
      \-f, 3

=> You can search by features

In [64]:

# search by features
[Tree node 'a' (-0x7ffff810443aa570)]
[Tree node 'a' (-0x7ffff810443aa570)]

=> Here is a quick list of useful functions

In [65]:

# get sister node =====> get_sisters()
sister = (t1&'a').get_sisters()
print("\nSISTERS of  a : ")
SISTERS of a : 
[Tree node 'b' (0x7efbbc55ab0)]

In [66]:

# get children  =====> get_children()
root_children = t1.get_children()
print("\n\nFIRST CHILD OF ROOT")

   /-|   \-b
  |  |
--|   \-c

In [67]:

# Get the  LCA (Latest Common Ancestor) of multiple node ====> get_common_ancestor()
lca = t1.get_common_ancestor(['a', 'b'])
print("\n\nLCA (a, b) : ")
LCA (a, b) : 


In [68]:

# RF (Robinson-Foulds) distance between t1 and t2.
# Recall that t1 and t2 have the same newick ...
rf = t1.robinson_foulds(t2)
print("\n\nRF DISTANCE between t1 and t2 :")
RF DISTANCE between t1 and t2 :

Introduction to tree visualization with ete

Data : a random tree with random branches

  • Tree rendering
  • Tree Style

In [71]:

from ete3 import Tree

# Generate a random tree (yule process)
t = Tree()
t.populate(8, names_library=list('ABCDEFGHIJKL'), random_branches=True)

print(t.get_ascii(attributes=['name', 'support'], show_internal=True))
               /-G, 0.47936
     /, 0.11319
    |         |          /-F, 0.53403
    |          \, 0.52094
-, 1.0                   \-E, 0.89822
    |          /-L, 0.27682
     \, 0.32620
              |          /-K, 0.50173
               \, 0.07320
                        |          /-J, 0.14208
                         \, 0.93141
                                  |         /-I, 0.05555
                                   \, 0.87512
                                            \-H, 0.81088

=> Trees can be saved as images. Supported format are png, pdf and svg.

In [74]:

t.render('tree.png', dpi=200)


=> You can use TreeStyle to change how the tree is displayed

In [75]:

from ete3 import TreeStyle

ts = TreeStyle()
ts.show_branch_length = True # show branch length
ts.show_branch_support = True # show support

# rotate the tree by 30 degree
ts.rotation = -30
t.render('tree2.png', tree_style=ts)


Let’s draw a circular tree now

In [76]:

ts.rotation = 0
ts.mode = "c" # use circular mode 
ts.arc_start = -180 
ts.arc_span = 180
t.render('tree3.png', tree_style=ts, w=500)


=> faces are wonderful

faces allow you to add graphical informations to a node. It can be a simple Text, an Image or a more useful information like a Chart or Sequence domains.

Here is the list of available faces :

In [77]:

# Adding face to Tree
from ete3 import faces
print([f for f in dir(faces) if 'Face' in f])
['AttrFace', 'BarChartFace', 'CircleFace', 'DynamicItemFace', 'Face', 'ImgFace', 'OLD_SequenceFace', 'PieChartFace', 'ProfileFace', 'RandomFace', 'RectFace', 'SeqMotifFace', 'SequenceFace', 'SequencePlotFace', 'StackedBarFace', 'StaticItemFace', 'TextFace', 'TreeFace']

Faces can be added at different areas around a node.


With Faces, you can actually make things like this (treeception) :


It’s also possible to define a layout function that will determine how a node will be rendered. Let’s see how to do that and in which cases this could be useful with the next example.

Application 1 : Duplication|Loss history of a gene familly

Data : genetree newick where I have already added a feature (states) :

  • states = 1 ==> internal node with duplication
  • states = 0 ==> internal node with speciation

In [80]:

from ete3 import Tree
t = Tree('annoted_trees', format=2)
print(t.get_ascii(show_internal=True, attributes=['name', 'states']))
      /-Dre_1, 0
   /, 0
  |  |   /-Cfa_1, 0
  |   \, 0
-, 1     \-Hsa_1, 0
  |   /-Dre_2, 0
   \, 0
      \-Cfa_2, 0

In [81]:

from ete3 import Tree, faces, TreeStyle
import utils

# Creates a layout function
def mylayout(node):
    if node.is_leaf():
        # add a face for its scientific name
        longNameFace = faces.TextFace(utils.get_scientific_name(node))
        faces.add_face_to_node(longNameFace, node, column=1)

        # add an image Face
        node.img_style["size"] = 0
        image = utils.get_image(
        faces.add_face_to_node(faces.ImgFace(image), node, column=0, aligned=True)
    # If node is a duplication node
    elif int(node.states) == 1:
        # Set the style as a green square
        node.img_style["size"] = 6
        node.img_style["shape"] = "square"
        node.img_style["fgcolor"] = "green"

    # If node is a speciation node
    else :
        # Set the style as a red circle
        node.img_style["size"] = 6
        node.img_style["shape"] = "circle"
        node.img_style["fgcolor"] = "red"

# And, finally, display the tree using the layout function
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = mylayout

t.render("tree4.png", dpi=600, tree_style = ts)


Application 2 : Phylogenetic tree, protein sequence and information content

Data :

  • An alignment
  • A tree constructed using that alignment (Actually those two were randomly generated)

In [82]:

from ete3 import PhyloNode, SequenceFace, faces, TreeStyle
from Bio import AlignIO
from Bio import Alphabet
from Bio.Align import AlignInfo
from utils import show_file

alignment = "alignment.fasta"
tree = "phylotree.nw"

# Open tree and link alignment to it
t = PhyloNode(tree)


In [83]:

# Compute Information content with Biopython
align =, 'fasta', alphabet=Alphabet.Gapped(Alphabet.IUPAC.protein))
summary_info = AlignInfo.SummaryInfo(align)        
total_ic_content = summary_info.information_content()
ic_content = summary_info.ic_vector.values()

# Set TreeStyle
ts = TreeStyle()
ts.branch_vertical_margin = 10
ts.allow_face_overlap = False
ts.show_scale = False
ts.show_leaf_name = False

# Align ic plot to TreeStyle header
ic_plot = faces.SequencePlotFace(ic_content, fsize=10, col_width=14, header="Information Content", kind='bar', ylabel="ic")
ts.aligned_header.add_face(ic_plot, 1) 

t.render("%%inline", tree_style=ts, dpi=300)


You can do a lot of things with ete if you take the time to learn how to use it. I didn’t have time to talk about ClusterNode, EvolNode or all the other great modules of ete, but I hope this post spark your interest and was useful to you.