Molecular Evolution and Phylogenomics
Graduate School of Health and Medical Sciences at University of Copenhagen
This is a specialised course. This means that 80% of the seats are reserved to PhD students enrolled at the Faculty of Health and Medical Sciences at UCPH and 20% og the seats are reserved to PhD students from other Danish Universities/faculties (except CBS).
The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee.
Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.
Learning objectives
A student who has met the objectives of the course will be able to:
1. Interpret phylogenetic trees and networks.
2. Engage with the fundamentals of sequence data.
3. Test a variety of hypotheses of comparative molecular evolution.
4. Experience the research process in the field of molecular evolution.
Content
This course will give students a broad understanding of phylogenetics, phylogenomics, and phylodynamics, via practice in these fields. Starting from the very basics, students will be exposed to depictions of trees and networks and taught to interpret graphics published on the topic. The most robust and commonly used methods of inferring phylogenetic trees are explained in detail, with an emphasis on the statistical theory and motivation for each. From the outset the course will be hands-on, placing the students in a position to critically evaluate choices in a project on molecular evolution.
In a mini project that can range fields of epidemiology, biodiversity, or linguistics, students will undertake the complete process of phylogenetic analysis from data preparation, through making inferences using sophisticated hierarchical models, finishing with interpretation and presentation of results.
With a heavy emphasis on hands-on research with real data sets, students will learn concepts and practice of sequence alignment, data cleaning and filtering, and inference of phylogeny and molecular evolutionary parameters, involving a range of methods and software.
In addition to basic methods of inference, students will be exposed to handling data sets with large numbers of genes and molecular dating. The course will therefore also cover the basics of Bayesian inference, common model hierarchies in phylogenetics and examples of their implementation.
Successful students will be able to report their phylogenetic procedures and results clearly and accurately for scientific publication.
Participants
This course is aimed at researchers interested in studying pathogens and biodiversity using genomic data. Attendees might come from any of a broad range of fields, but must be interested in analyses of multiple taxa, such as viruses, bacteria, plants, and vertebrates. A prior basic understanding of probability is strongly recommended.
Relevance to graduate programmes
The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:
Biostatistics and Bioinformatics
Immunology and Infectious Diseases
Public Health and Epidemiology
Language
English
Form
Lectures, computer exercises, group mini project
Course director
Associate Professor David Duchene
Department of Public Health, Section of Epidemiology
David.duchene@sund.ku.dk
Teachers
Associate Professor David Duchene
Department of Public Health, Section of Epidemiology
David.duchene@sund.ku.dk
Dates
26 - 30 October 2026
All days 9-16
Course location
CSS Building 7
Registration
Please register before 1 October 2026
Expected frequency
Once per year
Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules.
Applications from other participants will be considered after the last day of enrolment.