Introduction to Computational Evolutionary Biology

Preface

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

Setup

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
install.packages("BiocManager")

# Use BiocManager to install required packages
packages <- c(
    "treeio", 
    "ggtree", 
    "ggtree", 
    "ape", 
    "here", 
    "Biostrings",
    "MSA2dist", 
    "msa", 
    "phangorn", 
    "seqinr",
    "doubletrouble",
    "feature"
)

BiocManager::install(packages)

After that, you should have everything ready.