Application is open now here! (Extended deadline to 25th of October, 23:59 CEST. Applications submitted after the deadline will be placed on a waiting list. With the early deadline, we aim to give you enough time to secure funding, organise visa, travel etc.)
Workshop Information
The 2024 Workshop on Phylogenomics is being held January 21 to February 3, 2024 in Český Krumlov, Czech Republic. This is the 3rd edition of the workshop on Phylogenomics starting again after a four year hiatus.
This workshop brings together an international collection of faculty members and Workshop participants to study and discuss current ideas and techniques for exploring phylogenomics. The Workshop consists of a series of lectures, demonstrations and computer laboratories that cover theoretical and conceptual aspects of large-scale phylogenetics and phylogenomics, with a strong emphasis on data analysis.
The Workshop extends on topics developed in both the Workshop on Molecular Evolution and the Workshop on Genomics placing them in a phylogenomic framework. It places a strong focus on molecular phylogenetics performed at genome-wide scales (phylogenomics), and covers all aspects of phylogenomics workflows. The workshop will cover main aspects of phylogenomics: the reconstruction of species trees from large-scale genomics data. In addition, we will explore the use of phylogenomic data to 1) study species divergence and trait evolution patterns, 2) reconstruct and analyze genome-wide collections of species trees to detect orthology and paralogy, and 3) study genome dynamics along species trees.
The Workshop registration fee is $1,950. We provide approximately 90 hours of teaching during the two week workshop. Our price is therefore approximately $22 an hour. Note that this amount does not cover travel, lodging or boarding.
Many important details regarding fees and other information can be read on our FAQ page.
The Workshop on Phyloenomics 2024 is organised by:
Anna Karnkowska, University of Warsaw
Antonis Rokas, Vanderbilt University
Rosa Fernández, Institute of Evolutionary Biology (CSIC-UPF)
Toni Gabaldón, Barcelona Supercomputing Centre (BSC), and Institute for Research in Biomedicine (IRB)
Scott Handley, Washington University
Stay in touch:
- Join Our Newsletter (bottom of this page) to get announcements.
- You can also stay updated through twitter and facebook.
Week 1 : 21-27 January, 2024
| Date | Day | Time | Presenter | Topic | LOCATION |
|---|---|---|---|---|---|
| Jan 21 | Sunday | 18 – 22 | Everyone | Reception | Hotel Zlaty Andel |
| Jan 22 | Monday | 09 – 12 | Anna Karnkowska
Daniel Kintzl |
Introduction and Orientation,
Town Services |
Town Theatre |
| Monday | 14 – 17 | Workshop Team | Lab introduction | Town Theatre | |
| Monday | 19 – 22 | Everyone | Scientific speed networking | Egon Schiele Museum | |
| Jan 23 | Tuesday | 09 – 12 | Rosa Fernández | Introduction to Phylogenomics | Town Theatre |
| Tuesday | 14 – 17 | Workshop Team | Alignment and Alignment Trimming | House of Prelate | |
| Tuesday | 19 – 22 | Workshop Team | Tree Visualization & Tree Challenge | House of Prelate | |
| Jan 24 | Wednesday | 09 – 12 | Marina Houben | Introduction to Phylogenetics, and Orthology and Paralogy | House of Prelate |
| Wednesday | 14 – 17 | Marina Houben | Orthology and Paralogy Prediction lab | House of Prelate | |
| Wednesday | 19 – 22 | Workshop Team | Partitioning and Concatenation Laboratory workshop & data workshop | House of Prelate | |
| Jan 25 | Thursday | 09 – 12 | Olivier Gascuel | State-of-the-art methods and software used in phylogenomic inference | Town Theatre |
| Thursday | 14 – 17 | Erin Molloy | Coalescent methods in the context of phylogenomic inference lab | House of Prelate | |
| Thursday | 19 – 22 | Alexey Kozlov | RAxML software and phylogenomic analyses | House of Prelate | |
| Jan 26 | Friday | 09 – 12 | Hélène Morlon | Trait evolution on trees, and phenotypic and species diversification | Town Theatre |
| Friday | 14-17 | Erin Molloy | Coalescent methods in the context of phylogenomic inference lab | House of Prelate | |
| Friday | 19 – 22 | Alexey Kozlov | Green computing | House of Prelate | |
| Jan 27 | Saturday | 09 – 12 | Matthew Christmas | Evolution and genomic basis of shared and specialized traits in mammals | House of Prelate |
| Saturday | 14 – 17 | Aoife McLysaght | Phylogenetic inference in the context of Whole Genome Duplication | House of Prelate | |
| Saturday | 19 – 22 | Everyone | Town Tour
Workshop Dinner Party |
Town Square |
Week 2 : 28 January -3 February, 2024
| Date | Day | Time | Presenter | Topic | Location |
|---|---|---|---|---|---|
| Jan 28 | Sunday | All Day | Everyone | Free Day | Up to you! |
| Jan 29 | Monday | 09 – 12 | Antonis Rokas | Incongruence | House of Prelate |
| Monday | 14 – 17 | Jacob Steenwyk | Incongruence detection lab | House of Prelate | |
| Monday | 19 – 22 | Jordi Paps Montserrat | Using genome-level processes to solve tricky nodes in phylogenetics | House of Prelate | |
| Jan 30 | Tuesday | 09 – 12 | Toni Gabaldon | Gene family evolution | Town Theatre |
| Tuesday | 14 – 17 | Gytis Dudas | TBA | House of Prelate | |
| Tuesday | 19 – 22 | Everyone | Open Lab | House of Prelate | |
| Jan 31 | Wednesday | 09 – 12 | Laura Eme | Deep evolution of eukaryotes: problems and solutions from recent research | Town Theatre |
| Wednesday | 14 – 17 | Anna Karnkowska | TBA | House of Prelate | |
| Wednesday | 19 – 22 | Workshop Team | How to get programs, Summary/ Discussion on phylogenomic pipelines | House of Prelate | |
| Feb 1 | Thursday | 09 – 12 | Gergely Szöllősi | Horizontal Gene Transfer | Town Theatre |
| Thursday | 14 – 17 | Gergely Szöllősi | Horizontal Gene Transfer Lab | House of Prelate | |
| Thursday | 19 – 22 | Everyone | Open Lab | House of Prelate | |
| Feb 2 | Friday | 09 – 12 | Lisa Pokorny | Target Capture Sequencing Approaches in Phylogenomics | House of Prelate |
| Friday | 14 – 17 | Everyone | Round table discussions, T-shirts and certificates | Egon Schiele Museum | |
| Friday | 19:30 – 22 | Everyone | End of Workshop Party | You Decide! | |
| Feb 3 | Saturday | All Day | Everyone | Departure |