Joint Wellcome Trust-EMBL-EBI advanced course on Computational Molecular Evolution
This joint Wellcome Trust-EMBL-EBI advanced course aims to provide researchers with the theoretical knowledge and practical skills required to carry out molecular evolutionary analysis on their own data, as well as on data drawn from sequence databases. The course will combine basic assumptions and ideas fundamental to the field with discussion of cutting-edge methodologies, and is therefore relevant to researchers with a range of different experience levels.
Topics
- Interpretation of molecular phylogenetic trees
- Dataset assembly and sequence alignment
- Phylogenetic models and phylogeny reconstruction methods
- Parallel computing in phylogenetics
- Hypothesis testing in phylogenetics
- Estimating divergence times
- Coalescent model and inference from population data
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 29 April 2013 | ||
| 16:00 | Registration | |
| 17:00 | Welcome drinks ay Holiday Inn | |
| 18:00 | Dinner at Holiday Inn | |
| Day 2 - Tuesday 30 April 2013 | ||
| 08:30 | Introduction and overview of the course | |
| 10:00 | Coffee | |
| 10:30 | Introduction and overview of the course | |
| 12:30 | Lunch | |
| 13:30 | How to Interpret Molecular Phylogenetic Trees and Sequence Alignments | Aidan Budd, Brian Moore & Adrian Friday |
| 15:00 | Coffee | |
| 15:30 | How to Interpret Molecular Phylogenetic Trees and Sequence Alignments | Aidan Budd, Brian Moore & Adrian Friday |
| 17:30 | Coffee | Martin Embley |
| 18:00 | Keynote Lecture | |
| 19:00 | Supper | |
| 20:00 | UNIX/Windows command line basics; exercises | |
| Day 3 - Wednesday 1 May 2013 | ||
| 08:30 | How to Interpret Molecular Phylogenetic Trees and Sequence Alignments | Aidan Budd, Brian Moore & Adrian Friday |
| 10:00 | Coffee | |
| 10:30 | How to Interpret Molecular Phylogenetic Trees and Sequence Alignments | Aidan Budd, Brian Moore & Adrian Friday |
| 12:30 | Lunch | |
| 13:00 | Dataset Assembly and Sequence Alignment | Stephen Smith & Benjamin Redelings |
| 15:00 | Coffee | |
| 15:30 | Dataset Assembly and Sequence Alignment | Stephen Smith & Benjamin Redelings |
| 17:30 | Coffee | |
| 18:00 | Practicals | |
| 19:00 | Supper | |
| 20:00 | Additional practicals | |
| Day 4 - Thursday 2 May 2013 | ||
| 08:30 | Dataset Assembly and Sequence Alignment | Stephen Smith & Benjamin Redelings |
| 10:00 | Coffee | |
| 10:30 | Dataset Assembly and Sequence Alignment | Stephen Smith & Benjamin Redelings |
| 12:30 | Lunch | |
| 13:30 | Sanger Tour | |
| 14:30 | Coffee | |
| 15:00 | Dataset Assembly and Sequence Alignment | Stephen Smith & Benjamin Redelings |
| 17:30 | Coffee | |
| 18:00 | Supper | |
| 19:00 | Dataset Assembly and Sequence Alignment Practicals | |
| Day 5 - Friday 3 May 2013 | ||
| 08:30 | Easy Mathematics of Phylogenetic Trees | Olivier Gascuel |
| 10:00 | Coffee | |
| 10:30 | Phylogenetic Models | Brian Moore |
| 12:30 | Lunch | |
| 13:30 | Phylogeny-reconstruction methods: parsimony, distance, ML | Olivier Gascuel |
| 15:00 | Coffee | |
| 15:30 | Branch supports - Using PhyML | Maria Anisimova, Olivier Gascuel |
| 17:30 | Coffee | |
| 18:00 | Practicals | |
| 19:00 | Supper | |
| 20:00 | Additional Practicals | |
| Day 6 - Saturday 4 May 2013 | ||
| Free day | ||
| Day 7 - Sunday 5 May 2013 | ||
| 08:30 | Bayesian Methods to Infer Trees | Brian Moore |
| 10:00 | Coffee | |
| 10:30 | Using MrBayes | Brian Moore, Maria Anisimova |
| 12:30 | Lunch | |
| 13:30 | Parallel Computing Phylogenetics | Alexis Stamatakis |
| 15:00 | Coffee | |
| 15:30 | Parallel Computing Phylogenetics | Alexis Stamatakis |
| 17:30 | Coffee | |
| 18:00 | Keynote Lecture | John Huelsenbeck |
| 19:00 | Supper | |
| 20:00 | Additional Practicals | |
| Day 8 - Monday 6 May 2013 | ||
| 08:30 | Hypothesis testing in phylogenetics | Nick Goldman & Ziheng Yang |
| 10:00 | Coffee | |
| 10:30 | Hypothesis testing in phylogenetics | Nick Goldman & Ziheng Yang |
| 12:30 | Lunch | |
| 13:30 | Hypothesis testing in phylogenetics | Nick Goldman & Ziheng Yang |
| 15:00 | Coffee | |
| 15:30 | Hypothesis testing in phylogenetics | Nick Goldman & Ziheng Yang |
| 17:30 | Coffee | |
| 18:00 | Keynote Lecture | Antonis Rokas |
| 19:00 | Supper | |
| 20:00 | Additional Practicals | |
| Day 9 - Tuesday 7 May 2013 | ||
| 08:30 | Hypothesis testing in phylogenetics | Nick Goldman & Ziheng Yang |
| 10:00 | Coffee | |
| 10:30 | Hypothesis testing in phylogenetics | Nick Goldman & Ziheng Yang |
| 12:30 | Lunch | |
| 13:30 | Estimating Divergence Times | Jeff Thorne & Tracy Heath |
| 15:00 | Coffee | |
| 15:30 | Estimating Divergence Times | Jeff Thorne & Tracy Heath |
| 17:30 | Coffee | |
| 18:00 | Keynote Lecture | Carolin Kosiol |
| 19:00 | Supper | |
| 20:00 | Additional Practicals | |
| Day 10 - Wednesday 8 May 2013 | ||
| 08:30 | Coalescent model and inference from population data | Adam Leache & Bruce Rannala |
| 10:00 | Coffee | |
| 10:30 | Coalescent model and inference from population data | Adam Leache & Bruce Rannala |
| 12:30 | Lunch | |
| 13:30 | Coalescent model and inference from population data | Adam Leache & Bruce Rannala |
| 15:00 | Coffee | |
| 15:30 | Coalescent model and inference from population data | Adam Leache & Bruce Rannala |
| 17:30 | Coffee | |
| 18:00 | Practicals | |
| 19:00 | Supper | |
| 20:00 | Additional Practicals | |
| Day 11 - Thursday 9 May 2013 | ||
| 08:30 | Coalescent model and inference from population data | Adam Leache & Bruce Rannala |
| 10:00 | Coffee | |
| 10:30 | Coalescent model and inference from population data | Adam Leache & Bruce Rannala |
| 12:30 | Lunch | |
| 13:30 | Additional Topics (by request) | |
| 15:00 | Coffee | |
| 15:30 | Q & A and Student Presentations | |
| 19:30 | Course Dinner | |
| Day 12 - Friday 10 May 2013 | ||
| Departure from Cambridge | ||
Prerequisites
Applicants should be, at minimum, postgraduates engaged in relevant research. More experienced/advanced researchers are also encouraged to apply.
Cost
This is a residential course, without exception, and although the course is subsidised by the Wellcome Trust there is a charge of £1540 towards board and lodging for non-commercial applicants.The fee for commercial applicants is £3025.
Bursaries
Limited bursaries are available for non-commercial applicants (50 per cent of fee) and are subject to open competition. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).
Applications
Application forms for this course can now be completed online. Please click here to be redirected to the application portal. If you have any problems with the online application process, please email us.
Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your supervisor or head of department. A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline.
Deadlines
Deadline for applications: 16 November 2012
Full details regarding the course can be found here