Phylogenetics and -genomics Tutorial

Tutorial Description

This tutorial is part of the Phylogenomics-module in the Tools in Molecular Data Analysis course.

In Phylogenomics we use information from (almost) the whole genome to infer evolutionary relationship between species. The purpose of this module is to use and expand the practical skills that were taught in the shell-module to explore the strengths and limitations of phylogenomics. We go through a case study and use blast and phylogenetics to study genome evolution in this species.

What we will NOT do: go into detail about tree inference algorithms, or about methods to combine trees, such multi-species coalescence. If you want to know more about that, contact your teacher (see e-mail below) and she’ll happily refer you to material to help you on your way, depending on your specific questions and interests.

Contact person: Like Fokkens -


Prior knowledge that is required includes basic knowledge of the Bash shell (as taught in this Software Carpentry lesson) and basic knowledge on phylogeny, e.g. how to interpret a tree and a rough outline of the workflow to infer a tree.

To perform the analyses in this module, you need
  • Docker desktop

  • Shell Bash

  • a web browser

  • a text editor to keep a lab-journal.


During this tutorial you will work in teams. We will practice on how to keep a lab-journal for computational projects. During the analyses you do for this project, you are asked to keep a record to the best of your ability. At some point you will review the lab-journal of a peer (and someone will review yours) and give feedback. The goal is to raise awareness on how difficult it can be to reproduce someone else’s results. Importantly, ‘someone else’ includes your future self. You can find guidelines for keeping a lab-journal here.

A lab-journal contains the research questions asked, a detailed description of the experiments/analyses performed, a description of the results of your experiment, the conclusion you draw from the results (or a statement that you can not draw any conclusions, because your experiment failed) and further questions that are raised - very much like a report.

Because in this course we focus on reproducible science, your lab journal is the main part of the assignment. You can read more information on the Canvas page of the course.