November 8, 2019

Phylogenetic trees: back to basics


Phylogenetics is essential for comparing biological species and understanding biodiversity for conservation. This workshop will discuss the basic principles and methods of phylogenetic inference. It will demonstrate the use of standard tools to estimate phylogenetic trees from aligned sequence data or distance data to help participants make informed decisions about which methods to use in their own research.

PART A (8/11/19): Participants will be guided through exercises using Galaxy Australia and other tools, working with examples drawn from the recently published Oz Mammals Genomics data.

PART B (4/12/19): A subsequent Q&A session will offer the opportunity for participants to receive expert feedback on the application of their new knowledge to their own research data.

Associate Professor Michael Charleston will lead the training from the University of Tasmania, working simultaneously with groups at host universities and research institutes across Australia.


Topics covered:

  • what is a phylogeny, and what are the challenges in phylogenetic inference
  • the basics of phylogenetic analysis, including distance-based and maximum likelihood approaches
  • interpreting trees and analysing their robustness
  • phylogenetic networks
  • comparing phylogenies.

Topics not covered:

  • workflows from read data to phylogeny
  • ​multiple sequence alignment
  • Bayesian methods (MCMC, BEAST, MrBayes).

A second workshop is planned for early 2020 in which these more advanced topics will be covered. Receive notifications by subscribing here.


By successfully completing this workshop, you will be able to:

  • understand the underlying methodologies of phylogenetic estimation (and be able to confidently choose appropriate methods for their own data)
  • perform quality control on aligned sequences for the purpose of phylogenetic inference
  • apply current best practices using a range of appropriate software with data in the form of aligned molecular sequences
  • critically assess the quality of inferred evolutionary trees
  • interpret phylogenetic network methods and other measures of uncertainty.


This workshop is aimed at molecular biologists who want to know more about phylogenetic trees. The exercises we’ll cover are beginner level, but you should know how molecular sequence data is produced and what it looks like. Maybe you’ve even built phylogenetic trees before but want to know more about the principles behind the tools.

Prior to the workshop, participants must:

  • watch an ”Introduction to Galaxy” video
  • apply for a free Galaxy Australia account using an Australian university email address (
  • bring along your own WIFI enabled and install the following free software on their own laptops: SplitsTree 4 (


Participants will gather at a local venue and connect with the lead trainer via an online interactive presentation. The training will comprise a series of short presentations combined with guided hands-on exercises on participants’ own laptops. All hands-on exercises will be supported by trained local Facilitators, with live online help from experienced bioinformaticians.

The workshop will be coordinated by organised by the Australian Biocommons with the assistance of a network of Facilitators around Australia.

This event is part of a series of bioinformatics training events. If you’d like to hear when registrations open for other events, please subscribe to Australian Biocommons.