Introduction

Phylogenetics is the application of molecular sequencing to study the evolutionary relationship among organisms. The typical way to illustrate this process is through the use of phylogenetic trees. The computation of these trees from genomic data is an active field of research with many real-world applications.

We will take the practical approach mentioned in this book to a new level; most of the recipes here are inspired by a very recent study on the Ebola virus, which researched the recent Ebola outbreak in Africa. This study is called Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak from Gire et al published on Science and is available at http://www.sciencemag.org/content/345/6202/1369.short. Here, we will try to follow a similar methodology to arrive at similar results from the paper.

In this chapter, we will use DendroPy (a phylogenetics library) and Biopython. We will use DendroPy Version 3. Version 4 may be out when you read...