Visualizing phylogenetic data

In this recipe, we will discuss how to visualize phylogenetic trees. DendroPy only has simple visualization mechanisms based on drawing textual ASCII trees, but Biopython has quite a rich infrastructure, which we will leverage here.

Getting ready

This will require you to have completed all of the previous recipes. Remember that we have the files for the whole genus of the Ebola virus, including the RAxML tree. Furthermore, a simplified genus version will have been produced in the previous recipe. As usual, you can find this content in the Chapter07/Visualization.py notebook file.

How to do it...

Take a look at the following steps:

1. Let’s load all of the phylogenetic data:

   from copy import deepcopy
   from Bio import Phylo
   ebola_tree = Phylo.read('my_ebola.nex', 'nexus')
   ebola_tree.name = 'Ebolavirus tree'
   ebola_simple_tree = Phylo.read('ebola_simple.nex', 'nexus')
   ebola_simple_tree...