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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 Phylogenomics 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

Important information:

Competitions
  • As a tradition we have a T-shirt design competition! Best T-shirt design (one front and one back image) will feature on the Workshop on Phylogenomics 2024 T-shirts! Submit your design by Friday 26th at the latest! (For inspiration, check out previous designs by our sister workshop here!)
  • BINGO!
Code of conduct
PHYLOgenomics Faculty
Find your way around Český Krumlov
  • Český Krumlov town information
  • Map of the 2024 changes in Český Krumlov due to the bridge reparation – Check before arrival to choose the bus stop closest to your accomodation!!
  • Map of the main locations in the schedule (Save to your Google Maps!)
  • Map of some of the main Český Krumlov restaurants (Save to your Google Maps!)
  • Map of some of the main Český Krumlov bars (Save to your Google Maps!)
  • Map of Český Krumlov service points: shops, pharmacy, ATM, hospital (Save to your Google Maps!)
  • Map of the historic City Centre of Český Krumlov

 

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 Introduction & Orientation, City Information Town Theatre
Monday 14 – 17 Workshop Team: Gemma Martínez-Redondo & Karin Steffen Lab introduction & Unix House of Prelate
Monday 19 – 22 Everyone Scientific speed networking Krumlov mill
Jan 23 Tuesday 09 – 12 Rosa Fernández Introduction to Phylogenomics Town Theatre
Tuesday 14 – 17 Workshop Team: Marina Marcet-Houben & Jacob L Steenwyk Alignment and (lab intro) Multiple Sequence Alignment Trimming House of Prelate
Tuesday 19 – 22 Workshop Team: Michał Karlicki & Eduard Ocaña-Pallarès Tree Visualization & Tree Challenge House of Prelate
Jan 24 Wednesday 09 – 12 Marina Marcet-Houben Introduction to Phylogenetics, and Orthology and Paralogy Town Theatre
Wednesday 14 – 17 Workshop Team: Marina Marcet-Houben & Jacob L Steenwyk Orthology and Paralogy Prediction lab & (lab intro), Gene trees challenge House of Prelate
Wednesday 19 – 22 Workshop Team: Jacob L Steenwyk & Karin Steffen
(lab intro), Partitioning and Concatenation Laboratory workshop & Bonus data challenge (slides, tasks, data)
House of Prelate
Jan 25  Thursday 09 – 12 Olivier Gascuel State-of-the-art methods and software used in phylogenomic inference (part 1, part 2) Town Theatre
Thursday 14 – 17 Erin Molloy Coalescent methods in the context of phylogenomic inference lab House of Prelate
Thursday 19 – 22 Oleksiy 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 (day 2)
House of Prelate
Friday 19 – 22 Matthew Christmas Evolution and genomic basis of shared and specialized traits in mammals (lecture slides) (zipped data folder)
House of Prelate
Jan 27 Saturday 09 – 12 Aoife McLysaght Phylogenetic inference in the context of Whole Genome Duplication Town Theatre
Saturday 14 – 17 Oleksyi Kozlov Green computing Town Theatre
Saturday 19 – 22 Everyone Town Tour, Workshop Dinner Party Town Square

Krumlov mill

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 Town Theatre
Monday 14 – 17 Jacob Steenwyk Incongruence detection lab (intro slides) 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 Reticulate evolution, temporal resolution and custom data visualisations for BEAST analyses
House of Prelate
Tuesday 19 – 22 Eduard Ocaña-Pallarès , Gytis Dudas Open Lab: Phylobayes (intro), BEAST (instructions, data) NEW FILE TO DOWNLOAD
House of Prelate
Jan 31 Wednesday 09 – 12 Lisa Pokorny Target Capture Sequencing Approaches in Phylogenomics Town Theatre
Wednesday 14 – 17 Antonis Rokas &
Toni Gabaldon
Antonis’ lecture
Toni’s lecture
House of Prelate
Wednesday 19 – 22 Workshop Team Discussion on phylogenomic pipelines & tree thinking
House of Prelate
Feb 1 Thursday 09 – 12 Gergely Szöllősi Horizontal Gene Transfer (pt 1, pt 2)
Town Theatre
Thursday 14 – 17 Gergely Szöllősi Horizontal Gene Transfer Lab House of Prelate
Thursday 19 – 22 Everyone Open Lab: Workshop summary & How to install software
House of Prelate
Feb 2 Friday 09 – 12 Anna Karnkowska Unravelling complexity: Exploring the evolution of microbial eukaryotes through phylogenomics and phylogenetics Town Theatre
Friday 14 – 17 Everyone Round table discussions, T-shirts and certificates House of Prelate
Friday 19:30 – 22 Everyone End of Workshop Party You Decide!
Feb 3 Saturday All Day Everyone Departure

 

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