Phylogenomics workshop using IQ-TREE

The recent advent of next-generation sequencing techniques has led to the rapid accumulation of large amounts of phylogenomic / transcriptomic data. This is extremely useful in resolving many "deep phylogenetic" questions in the Tree of Life. At the same time however, it poses major computational challenges to analyse such Big Data, which most phylogenetic software cannot handle. Moreover, there is a need to develop more complex, probabilistic models to adequately capture realistic aspects of genomic sequence evolution.

These trends motivated the development of IQ-TREE. With a strong emphasis on phylogenomic inference its goals are:

  • Accuracy: Proposing novel computational methods that perform better than existing approaches.
  • Speed: Allowing fast analysis on big data sets and utilizing high performance computing platforms.
  • Flexibility: Facilitating the inclusion of new (phylogenomic) models and sequence data types.
  • Versatility: Implementing a broad range of commonly-used maximum likelihood analyses.


Workshop schedule

  • 9:00-9:15 Introduction
  • 9:15-10:30 Rob Lanfear - Sequence alignment, maximum-likelihood phylogenetics, model selection, tree search.
  • 10:30-11:00 Morning tea break
  • 11:00-12:30 Minh Bui - IQ-TREE practice
  • 12:30-14:00 Lunch
  • 14:00-15:30 Minh Bui - Partition models for phylogenomic data (theory & practice)
  • 15:30-16:00 Afternoon tea break
  • 16:00-17:00 Minh Bui - Concordance factors (theory & practice)



  • Basic knowledge of command lines.
  • Participants should bring their own laptop with the following software installed: Jalview, IQ-TREE and FigTree
  • They should also download an example alignment called 'example.phy' (from the download binary) and perform these steps: 
  1. View the alignment in Jalview
  2. Run this analysis in IQ-TREE: `iqtree -s example.phy`
  3. View the tree file output from IQ-TREE in FigTree

A 'Getting Started' tutorial can be found here. Please contact Minh Bui if you have any questions.


Suggested reading



  • Cost $40 (Full) & $20 (Student) - includes morning and afternoon teas (lunch is not provided however there is a small kitchen with fridge near the workshop room, and there is the Pop-up Village or Little Pickle nearby).
  • Closes 23 Nov, 2018

Information on parking at ANU can be found here and a visitor parking map here.

*ANU participants please note: We have been advised by ANU Finance that ANU staff and students shouldn't pay for ANU activities (which includes CBA events) using an ANU Purchase Card - you need to arrange a journal transfer. Please use the "Promotion code" IQTREE when you register (this will allow you to register without a credit card) and then email Finance and ask them to do a journal transfer of $40 (Full) or $20 (Student) to the CBA's GLC S415100201 from your chosen GLC.