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Pathogen Phylogenetics and Nextstrain

Course 4


15–17 January 2024


Prof. Dr. Richard Neher
Biozentrum, University of Basel, Switzerland

Dr. Emma Hodcroft
Nextstrain, Basel, Switzerland


CH – 3823 Wengen | Bühlstube

Course description

Though phylogenetic methods have been used for decades to better understand pathogen transmission and evolution, and aid in planning interventions, the COVID-19 pandemic and subsequent unprecedented number of SARS-CoV-2 sequences shed new light on the ways that phylogenetic and phylodynamic methods can aid in reducing the burden of infectious diseases. In this course, students will learn to use the Nextstrain software pipeline to analyze and visualise pathogen sequences, as well as how to interpret the results. We will start with the basics of microbial evolution, phylogenetic methods, and discuss how we can learn from sequence data about disease dynamics. In the practical part, participants will learn how to use Auspice to explore visual, interactive phylogenies, and how to use the Nextstrain toolset to analyze pathogen genomes. Students will do both a virus and bacterial tutorial to become familiar with basic analyses and explore how to adapt these to other pathogens. Finally, students will discuss common misconceptions and mistakes in analysis and interpretation. Exercises will be conducted in Python and shell commands. Previous basic experience in basic shell commands (changing directories, running commands, creating files) is necessary, and basic experience with any programming language will be helpful.

Course objectives

  • To run a basic Nextstrain Augur analysis on different pathogens
  • To become familiar with using Nextclade to check sequences and in navigating the Nextstrain Auspice visualization to explore results
  • To become aware of how to interpret results correctly and common mistakes made

Course audience

PhD students and post-doctoral researchers who want to learn the basics of phylogentics, how to run phylogenetic analyses using the Nextstrain software, and how to interpret the resulting phylogenies.

Course outline

The course runs over three days and consists of short lectures, computer demos, and practical sessions with real-data analysis. During the extended break in the afternoon, participants can review course material, read papers, or take part in social activities or outings.

Monday, 15 January 8:00 am – 12:00 pm | 4:30 pm – 6:30 pm
Tuesday, 16 January 8:00 am – 12:00 pm | 4:30 pm – 6:30 pm
Wednesday, 17 January 8:00 am – 12:00 pm | 1:00 pm – 3:00 pm

Day 1

  • Basics of microbial evolution
  • Introduction to phylogenetics methods
  • Using Auspice to visualize & explore phylogenetic trees
  • Nextclade tutorial & checking Nextstrain installations

Day 2

  • Introduction to the Nextstrain augur workflow
  • Viral and bacterial tutorials
  • Practice editing workflows

Day 3

  • Common mistakes & misconceptions in phylogenetic analyses
  • Adapting workflows to other pathogens


1.0 ECTS

Course materials

Students should bring their own portable computers with Nextstrain CLI installed. Instructions for doing this on Windows, Mac, and Linux can be found at

Onsite University of Bern IT staff provides support upon e-mail () request.

Course book

Course materials and slides will be made available via website during and after the course.

Course fee

PhD Bern: CHF 600
PhD other: CHF 800
Academic: CHF 1000
Industry: CHF 2000


  • There will be a pre-registration window from 24 August to 04 September 2023.
  • Within 10 days after this preliminary registration, we will let you know whether a place is available for you for the course you choose.


Book your accommodation separately. Please see recommendations for special prices.