The 2019 Workshop on Phylogenomics will be held in Český Krumlov, Czech Republic, from 20 January – 2 February. This will be the second version of the Workshop on Phylogenomics, which extends on topics developed in both the  Workshop on Molecular Evolution and the Workshop on Genomics placing them in a phylogenomic framework.

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 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.

A majority of the schedule is dedicated to hands-on learning activities designed by faculty and the workshop team. This interactive experience provides Workshop participants with the practical experience required to meet the challenges presented by modern evolutionary sciences.

The Workshop registration fee is $1,800. This amount does not cover travel, lodging or boarding. Many important details about this and other topics can be read on our FAQ page and a map of important locations: Workshop Guide.

A full schedule can be viewed below. Modifications and additions to the schedule may be made at any time prior to the beginning of the Workshop; however, the overall content and structure will remain largely the same.

The Workshop on Phylogenomics is organized by:

Toni Gabaldón, Center for Genomic Regulation

Scott Handley, Washington University

Anna Karnkowska, University of Warsaw

Antonis Rokas, Vanderbilt University



Week 1: 20-26 January 2019

Date Time Presenter Topic Location
20 Jan 6p – 10p Everyone Reception Hotel Zlatý Anděl
21 Jan 9a – 12p Antonis Rokas Introduction and Orientation Theater
2p – 5p Workshop Team Lab Introduction House of Prelate
7p – 10p Everyone Scientific Speed Networking Monastery
22 Jan 9a – 12p Antonis Rokas Introduction to Phylogenomics Theater
2p – 5p Workshop instructors (Lisa & Marina) Alignment and Alignment Trimming House of Prelate
7p – 10p Workshop instructors (Lisa & Marina) Tree Visualization House of Prelate
23 Jan 9a – 12p Toni Gabaldón Introduction to Phylogenetics, and Orthology and Paralogy Theater
2p – 5p Toni Gabaldón & Marina Marcet-Houben Orthology and Paralogy Prediction lab House of Prelate
7p – 10p Workshop instructors (Jacob) Partitioning and Concatentation Laboratory House of Prelate
24 Jan 9a – 12p Xiaofan Zhou Introduction to Methods and Software for Phylogenomics Theater
2p – 5p Alexey Kozlov RAxML Introduction and Laboratory House of Prelate
7p – 10p Stephen Crotty IQtree Introduction and Tutorial House of Prelate
25 Jan 9a – 12p Celine Scornavaca Non-Vertical Evolution and Phylogenetic Networks Theater
2p – 5p Celine Scornavaca Networks Lab House of Prelate
7p – 10p Xiaofan Zhou Phylobayes Intro and Practical House of Prelate
26 Jan 9a – 12p Laura Kubatko Coalescent Methods Theater
2p – 5p Laura Kubatko Coalescent Methods Lab House of Prelate
6p – 10p Everyone Workshop Social Event TBD

Week 2: 29 January – 4 February, 2019

Date Time Presenter Topic Location
27 Jan All Day Everyone Free Day Your choice!
28 Jan 9a – 12p Mario dos Reis Bayesian Phylogenetic Analysis Town Theater
2p – 5p Tracy Heath Molecular Clocks and Dating Analysis House of Prelate
7p – 10p Tracy Heath & Mario dos Reis Dating Analysis Lab II House of Prelate
29 Jan 9a – 12p Laszlo Garamszegi Trait evolution and ancestral state reconstruction Town Theater
2p – 5p Laszlo Garamszegi Trait evolution and ancestral state reconstruction House of Prelate
7p – 10p Everyone Open Lab House of Prelate
30 Jan 9a – 12p Jason Stajich Evolutionary Genomics Town Theater
2p – 5p Jason Stajich Evolutionary Genomics Practical House of Prelate
7p – 10p Everyone Open Lab House of Prelate
31 Jan 9a – 12p Jordi Paps Montserrat Evolution of Genomes and Gene Families Town Theater
2p – -3:15p

3:45p – 5p

Anna Karnkowska &

Martin Kolisko

Eukaryotic cell evolution: a phylogenetic perspective

Phylogenomics: resolving the tree of eukaryotes, new lineages, and phylogenetic artifacts

Town Theater
7p – 10p Everyone Open Lab House of Prelate
1 Feb 9a – 12p Gergely Szöllősi Horizontal Gene Transfer Town Theater
2p – 5p Gergely Szöllősi Horizontal Gene Transfer Lab House of Prelate
7p – 10p Everyone End of Workshop Party You Decide!
2 Feb All Day Everyone Departure