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

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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

Depo (map)

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