Detailed information about the course
| Title | Workshop BEAST: Reconstructing gene trees and species trees using BEAST and *BEAST - CLOSED |
| Dates | 2-6 February 2015 |
| Organizer(s) | |
| Speakers | Dr. Stephan Nylinder, Swedish Museum of Natural History (SE) Angela Cano, PhD student, Conservatoire et Jardin botaniques de Genève (CH) |
| Description | This course deals with Bayesian Phylogenetics and Species Tree Reconstruction, including issues on Molecular Dating and Biogeography.
This course aims to Understand What Causes What in a given analysis (an not to be fluent in setting up or modifying particular analysis file). People that will never perform an analysis can still benefit a great deal from the course when using the knowledge to scrutinize papers using BEAST or similar softwares. All participants will work in pairs during the workshops to enhance discussions. |
| Location |
University of Geneva |
| Map | |
| Credits | 2.5 |
| Information | PROGRAMMonday 2 (morning): Introduction to Bayesian phylogenetics using the BEAST package and MrBayes Monday 2 (afternoon): Fundamental functions and what to think about Tuesday 3 (morning): Principles of priors, substitution models, and tree priors Tuesday 3 (afternoon): Effects of over vs. under-parametersation, impact of tree priors Wednesday 4 (morning): Molecular dating and optimising traits Wednesday 4 (afternoon): Calibrating molecular phylogenies and estimating ancestral traits Thursday 5 (morning): Gene trees - species tree Thursday 5 (afternoon): Estimating and evaluating the species tree Friday 6 (morning): Bayes factors - what, why, how, when? Friday 6 (afternoon): 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. 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.
!IMPORTANT! Please bring your own laptops and download the following softwares: - BEAST 1.8.1 (included the associated BEAST softwares) - Tracer 1.6 - FigTree 1.4.1 - MrByes 3.2.3 When? |
| Expenses | Reimbursement: PhD students of the DPEE are eligible for reimbursement of incurred travel expenses by train (half-fare card, and 2nd class) and meals. Please send the original tickets (no copies, except for the general abonnement) and receipts with the reimbursement form to Caroline Betto-Colliard. |
| Registration | CUSO PhD students: On the MPS website through your MyCUSO account. Deadline of registration: 30 January 2015 |
| Places | 16 |
| Deadline for registration | |
| Joint activity |
|
short URL
URL onepage