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 & City Information Municipal Theater
2p – 5p Workshop Team
(Eric & Anna)
Lab introduction & how to use filezilla to download your data Prelatura
7p – 10p Everyone Scientific Speed Networking Monastery
22 Jan 9a – 12p Antonis Rokas Introduction to Phylogenomics Municipal Theater
2p – 5p Workshop instructors (Lisa & Marina) Alignment and Alignment Trimming Prelatura
7p – 10p Workshop instructors (Lisa & Marina) Tree Visualization & Tree Challenge Prelatura
23 Jan 9a – 12p Toni Gabaldón Introduction to Phylogenetics, and Orthology and Paralogy Municipal Theater
2p – 5p Toni Gabaldón & Marina Marcet-Houben Orthology and Paralogy Prediction lab Prelatura
7p – 10p Workshop instructors (Jacob) Partitioning and Concatentation Laboratory

workshop & data workshop

challenge & data challenge

24 Jan 9a – 12p Xiaofan Zhou Introduction to Methods and Software for Phylogenomics Municipal Theater
2p – 5p Alexey Kozlov RAxML-NG Introduction and Laboratory Prelatura
7p – 10p Stephen Crotty IQ-tree Introduction and Tutorial Prelatura
25 Jan 9a – 12p Celine Scornavacca Non-Vertical Evolution & Phylogenetic Networks Municipal Theater
2p – 5p Celine Scornavacca Networks Lab Tutorial & data Prelatura
7p – 10p Xiaofan Zhou Phylobayes Intro & Tutorial Prelatura
26 Jan 9a – 12p Laura Kubatko Coalescent Methods Municipal Theater
2p – 5p Laura Kubatko Coalescent Methods Lab Prelatura
6p – 10p Everyone Workshop Dinner and party DEPO

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 Municipal Theater
2p – 5p Tracy Heath Molecular Clocks and Dating Analysis Prelatura
7p – 10p Tracy Heath & Mario dos Reis Bayesian MCMC Tutorial & scripts

MCMCTree tutorial & MCMCTree presentation

29 Jan 9a – 12p Laszlo Garamszegi Trait evolution and ancestral state reconstruction Municipal Theater
2p – 5p Laszlo Garamszegi Trait evolution and ancestral state reconstruction lab Prelatura
7p – 10p Jacob

Tracy Heath


Internode certainty and concordance factors tutorial & data


ETE3 tutorial & tree1 tree2

30 Jan 9a – 12p Jason Stajich Evolutionary Genomics Municipal Theater
2p – 5p Jason Stajich Evolutionary Genomics Practical & tutorial Prelatura
7p – 10p Marina



How to get programs


Discussion on phylogenomic pipelines

31 Jan 9a – 12p Jordi Paps Montserrat Reconstructing Ancestral Genomes to Understand Major Transitions Municipal Theater
2p – -3:15p

3:45p – 5p

Martin Kolisko


Anna Karnkowska

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

Eukaryotic cell evolution

Municipal Theater
7p – 10p Everyone Open Lab Prelatura
1 Feb 9a – 12p Gergely Szöllősi Horizontal Gene Transfer Municipal Theater
2p – 5p Gergely Szöllősi Horizontal Gene Transfer Lab Prelatura
7p – 10p Everyone End of Workshop Party Egon Schiele Café
2 Feb All Day Everyone Departure