Visualizing phylogenetic data
Here, 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.
Getting ready
This will require all the previous recipes. Remember that we will have files for the whole genus Ebola virus, including the RAxML tree. Furthermore, there will be a simplified genus version produced in the previous recipe.
Biopython uses matplotlib and graphviz as alternative backends. Graphviz is a graph visualization tool (do not confuse graph, the mathematical construct with a chart). While you should have matplotlib installed, you will need to install graphviz (http://www.graphviz.org/) and pygraphviz (http://pygraphviz.github.io/). Graphviz is available on Ubuntu and Linux (package graphviz). Pygraphviz can be installed using pip.
As usual, you can find this content in the 05_Phylo/Visualization.ipynb notebook.