Introduction to Computational Evolutionary Biology


Fabricio Almeida-Silva and Yves Van de Peer


January 1, 2023


This book aims to provide learners with a hands-on introduction to Computational Evolutionary Biology, and the materials here are used in the practical lessons of the courses C003709A - Evolutionary Biology and C000500A - Bioinformatics 2 at Universiteit Gent, taught by Dr. Yves Van de Peer and Fabricio Almeida-Silva.

Each book chapter represents the contents of a practical lesson from the UGent courses, and they serve both as a guide during the lessons and as a reference to go back later.

The book will cover:

  1. Introduction to the R programming language
  2. Data structures for Evolutionary Biology in R
  3. Multiple Sequence Alignment (MSA) and distance-based phylogeny inference
  4. Maximum likelihood-based phylogeny inference
  5. Analyses of gene and genome duplication


To run the code in this book, you will need to install:

  1. R (>=4.2.0): go to the CRAN website, choose your OS (Windows, Linux, or macOS), and follow the installation instructions.

  2. RStudio Desktop: go to the RStudio website and download the installer for your OS.

  3. IQ-TREE: go to the IQ-TREE download page and follow the installation instructions for your OS.

After installing R and RStudio, you will need to install some required R packages. To do that, open RStudio and execute the code below in your console:

# Install BiocManager

# Use BiocManager to install required packages
packages <- c(


After that, you should have everything ready.