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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

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: parsimony, 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

 

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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