Phylogenetics

Phylogenetics is the application of molecular sequencing that is used 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.

In this book, we will take the practical approach that is mentioned to a new level: most of the recipes here are inspired by a recent study on the Ebola virus, researching the recent Ebola outbreak in Africa. This study is called Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak, by Gire et al., published in Science. It is available at https://pubmed.ncbi.nlm.nih.gov/25214632/. Here, we will try to follow a similar methodology to arrive at similar results to the paper.

In this chapter, we will use DendroPy (a phylogenetics library) and Biopython. The bioinformatics_phylo Docker image includes all the...