Workshop BEAST: Reconstructing gene trees and species trees using BEAST and *BEAST

2-6 February 2015

Dr. Stephan Nylinder, Chercheur, Swedish Museum of Natural History, Stockholm, Sweden Angela Cano, Doctorante UNIGE, en thèse aux Conservatoire et Jardin botaniques

Bayesian phylogenetics and species tree reconstruction, including issues on molecular dating and biogeography. All participants will work in pairs during the workshops to enhance discussions. The course is not about training to be fluent in setting up and modifying particular analysis files, but understanding what causes what in a given analysis. Even someone who will never perform an actual analysis can still benefit a great deal from the course when using the knowledge to scrutinize papers using BEAST or similar softwares.

University of Geneva, Auditorium de Battelle (Centre Universitaire Informatique), Bâtiment A, rez de chaussée

Map

Workshop BEAST February 2-6 2015

Monday 2, 10-12am - Presentation: Introduction to Bayesian phylogenetics using the BEAST package and MrBayes

Monday 2, 1-4pm - Workshop: Fundamental functions and what to think about

Tuesday 3, 9-12am - Presentation: Principles of priors, substitution models, and tree priors

Tuesday 3, 1-4pm - Workshop: Effects of over vs. under-parametersation, impact of tree priors

Wednesday 4, 9-12am - Presentation: Molecular dating and optimising traits

Wednesday 4, 1-4pm - Workshop: Calibrating molecular phylogenies and estimating ancestral traits

Thursday 5, 9-12am - Presentation: Gene trees - species tree

Thursday 5, 1-4pm - Workshop: Estimating and evaluating the species tree

Friday 6, 9-12am - Presentation: Bayes factors - what, why, how, when?

Friday 6, 1-4pm - Workshop: Calculating and evaluating Bayes factors

 This setup builds on a very appreciated and successful course Dr Stephan Nylinder (Swedish Museum of Natural History, Stockholm) held in Olso in May 2014, with some modifications. Participants are required to bring their own laptops with the latest version of the required softwares installed (list below). The workshop will center on BEAST mostly because of the simplicity of explaining concepts using the GUI. The take-away from the course applies to any Bayesian software. Even if participants are usually encouraged to bring their own datasets, this course is entirely built on everyone working with the exact same data provided by the teacher. Rather than making a single test per workshop, the dataset is chosen and designed to run quickly on any computer multiple times in order to extensively explore the issues at hand.

The course will not focus on sequence alignment or model testing, even though such issues will be mentioned throughout the course.

Preliminary list of softwares:

-BEAST 1.8.1 (including the associated BEAST softwares)

-Tracer 1.6

-FigTree 1.4.1

-MrBayes 3.2.3

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