Basic Phylogeny Tutorial for command-line

March 01, 2016 | 1 Minute Read

First of all, Happy New Year!

With a new year, comes a new position. On the back of my recent talk at the Robinson Research Institute, University of Adelaide, I recently interviewed for the Bioinformatics leader position and was successful in getting the job. So after changing from Agricultural Genomics to Ancient DNA, I’m now completely changing track and working in Medical Science, or more specifically, in Pregnancy and Early Childhood Health. I’m very fortunate to be given the opportunity and I’m excited to begin working on the dark-side of genomics research (….humans!). My role will be as core-facility manager of Bioinformatics, meaning that I’ll collaborate with researchers within the institute on Bioinformatics projects, as well as working on some of my own research goals.

Additionally, half of my time is going to be used with the University of Adelaide’s Bioinformatics Hub, helping out students and researchers at the University who do not have access to Bioinformatics support. One part of that is creating tutorials and workshop material for students to use.

Many students at the University need support to run basic phylogenetic analysis from the command-line using Bayesian Inference or Maximum Likelihood methods, so I recently created a very basic tutorial on running multiple sequence alignment and tree building programs from a laptop. By taking 24 Marsupial whole mitochondrial genomes, the tutorial uses MAFFT and RAxML to create a basic bootstrapped tree. Like I said, very basic, but includes some principles such as editing alignments and converting between formats thats aimed at a researcher that is just getting familiar with the command-line interface.

If you’d like to use the tutorial or are interested in any of our current projects at the Bioinformatics Hub, check out the github repository here. Once I have some more time, I’ll likely expand on this with some more complex concepts and bash programming. If you have any comments, please email me at We’re very new to using github for tutorial management so I’m always happy for suggestions