Introduction to Pathogen Phylogenetic Analysis Workshop 21-22 November 2016

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 Sebastián Duchêne and Jane Hawkey from the Centre for Systems Genomics of the University of Melbourne. The workshop will consist of two modules. The first module will provide a basic framework to analyse molecular data and interpret phylogenetic trees and other parameters. The second module involves Bayesian methods and phylogenetic epidemiology. Some familiarity with molecular evolution and experience using the command line is useful but not essential. Participants are encouraged to bring data sets and questions to discuss potential analyses using phylogenetic methods.


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:


PhyML (


Tracer (

FigTree (

TempEst (

R (

Rstudio 1.0 (

The program can be found here.

Venue West room, University House @The Woodward ( University of Melbourne 185 Pelham St, Carlton, 3052