Workshop on Phylogenomics

2024

Český Krumlov, Czech Republic

Sessions

Participants

Countries

21 faculty

Instructors

Jacob L. Steenwyk· UC BerkeleyEduard Ocaña-Pallarès· Barcelona Supercomputing Center, SpainGemma Martínez-Redondo· Institute of Evolutionary Biology (IBE, CSIC-UPF) in BarcelonaMichał Karlicki· University of Warsaw, PolandKarin Steffen· Vanderbilt UniversityEric Salomaki· Institute of Parasitology, Czech Academy of Science, Czech RepublicRosa Fernández· Center for Genomic Regulation, SpainMarina Marcet-Houben· Center for Genomic Regulation, SpainMiguel Naranjo-Ortiz· Center for Genomic Regulation, SpainLisa Pokorny· Royal Botanic Gardens, Kew, UK

Date

Time

Topic

Type

Presenter(s)

22nd Jan

09-12

Introduction & Orientation

Orientation

Anna Karnkowska

14-17

Lab introduction & Unix

Practical

Gemma Martínez-Redondo, Karin Steffen

23rd Jan

09-12

Introduction to Phylogenomics

Lecture

Rosa Fernández

14-17

Alignment and Multiple Sequence Alignment Trimming

Practical

Marina Marcet-Houben, Jacob L Steenwyk

19-22

Tree Visualization & Tree Challenge

Practical

Michał Karlicki, Eduard Ocaña-Pallarès

24th Jan

09-12

Introduction to Phylogenetics, Orthology and Paralogy

Lecture

Marina Marcet-Houben

14-17

Orthology and Paralogy Prediction lab

Practical

Marina Marcet-Houben, Jacob L Steenwyk

19-22

Partitioning and Concatenation Laboratory

Practical

Jacob L Steenwyk, Karin Steffen

25th Jan

09-12

State-of-the-art methods and software in phylogenomic inference

Lecture

Olivier Gascuel

14-17

Coalescent methods in phylogenomic inference lab

Practical

Erin Molloy

19-22

RAxML software and phylogenomic analyses

Practical

Oleksiy Kozlov

26th Jan

09-12

Trait evolution on trees, phenotypic and species diversification

Lecture

Hélène Morlon

14-17

Coalescent methods lab day 2

Practical

Erin Molloy

19-22

Evolution and genomic basis of shared and specialized traits in mammals

Lecture

Matthew Christmas

27th Jan

09-12

Phylogenetic inference in Whole Genome Duplication context

Lecture

Aoife McLysaght

14-17

Green computing

Practical

Oleksyi Kozlov

29th Jan

09-12

Incongruence

Lecture

Antonis Rokas

14-17

Incongruence detection lab

Practical

Jacob Steenwyk

19-22

Using genome-level processes to solve tricky nodes in phylogenetics

Lecture

Jordi Paps Montserrat

30th Jan

09-12

Gene family evolution

Lecture

Toni Gabaldon

14-17

Reticulate evolution, temporal resolution and custom data visualisations

Lecture

Gytis Dudas

19-22

Open Lab: Phylobayes and BEAST

Practical

Eduard Ocaña-Pallarès, Gytis Dudas

31st Jan

09-12

Target Capture Sequencing Approaches in Phylogenomics

Lecture

Lisa Pokorny

14-17

Joint lecture

Lecture

Antonis Rokas, Toni Gabaldon

19-22

Discussion on phylogenomic pipelines & tree thinking

Discussion

Workshop Team

1st Feb

09-12

Horizontal Gene Transfer

Lecture

Gergely Szöllősi

14-17

Horizontal Gene Transfer Lab

Practical

Gergely Szöllősi

19-22

Open Lab: Workshop summary & software installation

Practical

Workshop Team

2nd Feb

09-12

Unravelling complexity: Exploring the evolution of microbial eukaryotes

Lecture

Anna Karnkowska