A quick overview on phylogenetics

Useful resources for molecular phylogenetics

  • Sydney Phylo Workshop by Simon Ho provides some excellent lecture notes and workshops with dataset
  • Phylogenetic Biology by Casey Dunn at Brown University is a great source of lecture and practical material. It also has a an extensive list of extra resources and useful links to reading material
  • RevBayes github page has a wealth of information specifically around the software but also includes some general phylogenetics material as well. Tutorial pages available here, a example of workshop page on molecular phylogenetics and fossil data available here
  • Taming the BEAST workshops around the use of BEAST software for Phylogenetics
  • Bayesian MCMC phylogenetics tutorial in R - for those wanting an R interface for their Phylogenetics
  • Collection of tutorials on phylogenetics by Michael Matschiner. This goes through the workflow from sequence analysis through to dating and more

Broadly conducting a phylogenetic analysis can be broken down in the following steps:

  1. Obtain sequences (e.g. your own sequences - ensure you perform approriate QC methods, or reference sequences from Genbank etc)
  2. Align sequences
  3. Decide on appropriate method and model - this will differ depending on your study question, data available, gene(s), length of sequence, type of data (i.e. nucleotide, amino acid etc)
    • You will likely need to use some program to help you decide on most appropriate model
  4. Conduct phylogeny recontsruction (with or without bootstrap/node support)
  5. Visualize and edit tree
 

Work by Siobhon Egan

siobhon.egan@murdoch.edu.au