Bioinformatics with Python Cookbook

Chapter 6. Phylogenetics

In this chapter, we will cover the following recipes:

• Preparing the Ebola dataset
• Aligning genetic and genomic data
• Comparing sequences
• Reconstructing phylogenetic trees
• Playing recursively with trees
• Visualizing phylogenetic data

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 ...