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Molecular phylogenetics

EBI

 

Description

The course will provide training for bench-based biologists to use molecular data to construct and interpret phylogenies, and test their hypotheses. Delegates will gain hands-on practice of using a variety of programs freely available online and commonly used in molecular studies, interspersed with some lectures.

 

Trainers

Asif Tamuri, EMBL-EBI

 

Audience and Prerequisites

  • Limited knowledge of the field of molecular evolution
  • Some experience of examining DNA/protein sequence data
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals

 

Syllabus, Tools and Resources

During this course you will learn about:

  • The principles of phylogenetics and how to reconstruct phylogenetic trees from molecular data
  • The different methods for phylogenetic reconstruction: distance-based, maximum likelihood, Bayesian
  • How to interpret reconstructed trees and assess their robustness
  • How to test hypotheses with respect to trees and decide which model to use for tree inference
  • Statistical methods to detect positive selection in coding sequences
  • How to use Bayesian methods for divergence time estimation

 

Learning Objectives

After this course you should be able to:

  • Reconstruct your own trees from data, choosing an appropriate set of tools and models
  • Have an overview of the software available for phylogenetic reconstruction
  • Know about the advantages and disadvantages of different phylogenetic reconstruction methods and make an informed choice
  • Know how to interpret the results with regards to evolutionary information, robustness and potential inaccuracies

 

Links

Book Here

 

Timetable

Time Topic
Day 1
09:00 Intro evolution & phylogenies
09:30 Interpreting phylogenies
11:00 Coffee
11:30 Parsimony & distance based phylogenetics (I)
12:30 Lunch
13:30 Parsimony & distance based phylogenetics (II)
14:15 From phenotypic to genomic features: Sequence alignments
15:00 Coffee
15:30 File formats in phylogenetics & tree visualisation
16:15 Genomic distance measures / Jukes Cantor
17:00 End
Day 2
09:00 Maximum Likelihood Phylogenetics
10:30 Coffee
11:00 Tree reconstruction: Practical
12:30 Lunch
13:30 Hypothesis testing
15:00 Coffee
15:30 Hypothesis testing: Practical
17:00 End
Day 3
09:00 Tree robustness: The bootstrap
10:30 Coffee
11:00 Tree robustness: Practical
12:30 Lunch
13:30 Positive selection
15:00 Coffee
15:30 Positive selection: Practical
17:00 End & Feedback
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