In this recipe, we will discuss how to visualize phylogenetic trees. DendroPy has only simple visualization mechanisms based on drawing textual ASCII trees, but Biopython has quite a rich infrastructure, which we will leverage here.
This will require you to have completed all of the previous recipes. Remember that we have the files for the whole genus 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 Chapter06/Visualization.ipynb
Notebook file.
Take a look at the following steps:
- Let's load all 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.name = 'Ebolavirus simplified tree'
For all of the trees that we read, we will change the name...