This course will provide students with a practical grounding in phylogenetic techniques. The course will consist of two one day workshops and project work defined partially by the student. By the end of the course the student should be able to build a phylogenetic tree for an organism of interest and confidently describe the result. En studerende, der fuldt ud har opfyldt kursets mål, vil kunne:

• Explain the different types of data that can be used to infer a tree. Understand the advantages of using DNA or protein sequences.
• Create a simple distance matrix and draw simple trees by hand.
• Use web based software to identify homologues, align sequences and infer phylogenetic trees and have a generally knowledge of the command line tools available and use these techniques to infer trees for genes of interest.
• Avoid common errors that can occur during alignment and inference.
• Confidently identify common phylogenetic patterns such as: polyphyly, paraphyly, monophyly, polytomy and understand the differences between orthologues, paralogues and homologues.
• Critically examine the quality of phylogenetic trees, including an understanding of the importance of outgroups and the difference between a rooted and unrooted tree understand the differences between likelihood, bootstrap, and consensus scores.
• Explain the difference between species and gene trees and some of the difficulties involved with inferring species trees.
• Describe the uses and difficulties associated with genome scale phylogenetic reconstruction.
• Test phylogenetic models.
• Write a partition file for a small number of genes.
• Describe the uses and potential pitfalls of ancestral state reconstruction, dating phylogenetic trees.
• Deliver a 5-minute presentation on the project work, describing the evolutionary relationships of a gene or organism of interest, specifically commenting on the quality of the phylogenetic inference, and giving a brief perspective on their results.

The five sessions will be organized over two days as follows:

DAY ONE:
1. Introduction
A short introduction to key concepts in phylogenetics. Students will construct a simple tree by hand. Additional time will be spent discussing students’ projects and their specific needs from the course.
2. From Sequences to Trees
The process of building a phylogenetic tree for a gene of interest. Finding homologues, aligning sequences and inferring phylogenetic trees. Students will also decide on a project to work on for the final session.
3. Interpreting Trees
The basics of interpreting phylogenetic trees. Interpreting evolutionary patterns and describing the quality of the inference. Time will also be spent helping the students with their individual projects.

DAY TWO:
4. Advanced Phylogenetic Techniques
More advanced phylogenetic analyses, including multi-locus trees and ancestral state reconstruction.
5. Presentation Session

Students will present their project work, demonstrating their understanding of concepts covered throughout the course. 1. Kapli P, Yang Z, Telford MJ. Phylogenetic tree building in the genomic age. Nature Reviews Genetics. 2020.
2. Jacques F, Bolivar P, Pietras K, Hammarlund EU. Roadmap to the study of gene and protein phylogeny and evolution—A practical guide. PLOS ONE, 2023
3. Ziemert N, Jensen PR. Phylogenetic Approaches to Natural Product Structure Prediction. In: Methods in Enzymology, 2012.
4. Booth TJ, Shaw S, Cruz-Morales P, Weber Y. getphylo: rapid and automatic generation of multi-locus phylogenetic trees. BMC Bioinformatics, 2025. 03. juli, 2025