'Introduction to Pathogen Phylogenetic Analysis' Workshop

Introduction to Pathogen Phylogenetic Analysis

Monday 20 – Wednesday 22 November, 2017

Overview
This workshop will provide an introduction to phylogenetic analyses of infectious pathogens. It will cover basic concepts in phylogenetic analysis and practical sessions using popular software packages and empirical data. The workshop will be run by Dr Sebastian Duchene, Jane Hawkey (Department of Biochemistry & Molecular Biology and Bio21 Institute, University of Melbourne). Supported by a CBRI seed grant.

The workshop will consist of two modules and two research seminars. The first module will provide a basic framework to analyse molecular sequence data and to infer phylogenetic trees and other evolutionary parameters. The second module will introduce Bayesian methods and phylogenetic epidemiology. Some familiarity with molecular evolution and experience using the command line is useful but not essential. To illustrate some cutting-edge applications of phylogenetic methods, Dr John-Sebastian Eden (University of Sydney) and Dr Remco Bouckaert (University of Auckland) will give seminars about their research.

Computing
The practical sessions will consist of analyses of publicly available data sets. We will use various software packages freely available online, and which can be installed in Windows, Mac, and UNIX platforms. Please bring a laptop and install the following packages before attending the workshop:

  • MEGA (megasoftware.net)
  • PhyML (http://www.atgc-montpellier.fr/phyml/)
  • BEAST2 (http://beast2.org)
  • Tracer (tree.bio.ed.ac.uk/software/tracer/),
  • FigTree (tree.bio.ed.ac.uk/software/figtree/)
  • TempEst (tree.bio.ed.ac.uk/software/tempest/)
  • R (https://www.r-project.org)
  • Rstudio 1.0 (www.rtudio.com)

The Eventbrite Invitation is now live (see link below), please email any dietary requirements to the CBRI Academic Convenor, Dr Andrew Siebel.

Full registration (includes 3-day workshop, lunch, afternoon tea & social event) - $120
Student registration (includes 3-day workshop, lunch, afternoon tea & social event) - $90 *Full-time students only

Register here: https://www.eventbrite.com/e/introduction-to-pathogen-phylogenetics-analysis-workshop-tickets-38486604470

Program

Day 1 - Monday 20 November

09:15 – 09:30  Arrival

09.30 – 10.30  Lecture 1.1: Introduction to molecular phylogenetics

10:30 – 11:00  Practical 1a: Sequence alignment in MEGA

-- Coffee break --

11:30 – 12:30  Lecture 1.2: Substitution models

-- Lunch --

13.30 – 14:15  Lecture 1.3: Phylogenetic methods

14:15 – 14:45  Practical 1b: Substitution model selection in MEGA

14:45 – 15:15  Practical 1c: Maximum likelihood analysis in PhyML

15:30 – 16:30  Public seminar by Dr John-Sebastian Eden (Agar Theatre)

Day 2 - Tuesday 21 November

09:15 – 09:30  Arrival

09:30 – 10:15  Lecture 2.1: The molecular clock

10:15 – 11:00  Practical 2a: Assessing temporal structure in TempEst

-- Coffee break --

11:30 – 12:30  Lecture 2.1: Bayesian phylogenetics

-- Lunch --

13.30 – 14.30  Lecture 2.2: Priors in Bayesian Phylogenetics

14:30 – 15:00  Practical 2b: Markov Chain Monte Carlo

15:00 – 15:30  Lecture 2.3: Demographic priors and model selection

15:30 – 16:30  Practical 3a: Molecular dating using BEAST

Day 3 – Wednesday 22 November

09:15 – 09:30  Arrival

09:30 – 10:00  A tour of BEAST2 (Remco Bouckaert)

10:00 – 11:00  Lecture 3.1: Infectious disease phylodynamics

-- Coffee break --

11:30 – 12:30  Practical 3a: Phylodynamics in BEAST Coalescent and Birth-Death models

-- Lunch --

13:30 – 14:30  Practical 3b: Phylodynamics in BEAST Birth-Death SIR

14:30 – 15:30  Phylogenetics clinic (Remco Bouckaert)

15:45 – 16:45  Public Seminar by Dr Remco Bouckaert (Agar Theatre)

17:30 – 19:00  Social event at Naughtons

Venues
Lectures and practical sessions: Project Room 253, Arts West North Wing, University of Melbourne, Parkville

Public seminars: Agar Theatre, Biosciences 4, University of Melbourne, Parkville

Social event: Naughtons Parkville Hotel, Royal Parade, Parkville


Useful references

  • An Introduction to Molecular Evolution and Phylogenetics Bromham (2016) Oxford University Press.
  • Bayesian Evolutionary Analysis with BEAST Drummond and Bouckaert (2015) Cambridge University Press.
  • Molecular Evolution: A Statistical Approach Yang (2014) Oxford University Press.
  • Estimating evolutionary timescales using the molecular clock Ho & Duchene (2014) Mol Ecol 23: 5947–5965.
  • Molecular phylogenetics: principles and practice Yang & Rannala (2012) Nat. Rev. Genet. 13: 303-314.
  • A Biologist’s guide to Bayesian phylogenetic analysis Nascimento, dos Reis & Yang  (2017). Nat. Ecol. Evol. 1: 1446-1454.