Phylogenetics
genomics
phylogenetics
Notes on phylogenetics
Phylogenetics
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
- Data Integration, Manipulation and Visualization of Phylogenetic Trees
Broadly conducting a phylogenetic analysis can be broken down in the following steps:
- Obtain sequences (e.g. your own sequences - ensure you perform approriate QC methods, or reference sequences from Genbank etc)
- Align sequences
- 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
- Conduct phylogeny recontsruction (with or without bootstrap/node support)
- Visualize and edit tree