Phylogenetics 101, a three-hour foundation.
A compact workshop for upper-level undergraduates and early graduate students who need to read a tree, build one, and know when to trust the result. Tree thinking, sequence alignment, inference by neighbor-joining, maximum likelihood, and Bayesian methods, and how to assess support. Slides, recordings, and practice datasets are linked below.
What the workshop covers
Scope Five topics, three hours, hands-on From tree thinking to assessment, with the software that does the work.
- Tree thinking. Understanding evolutionary relationships and reading phylogenetic trees.
- Sequence alignment. Methods for aligning DNA and protein sequences for phylogenetic analysis.
- Inference methods. Neighbor-joining, maximum likelihood, and Bayesian approaches to building trees.
- Tree assessment. Bootstrapping, posterior probabilities, and how to judge confidence.
- Software. Practical experience with the packages actually used in published phylogenetics.
The workshop assumes a basic grasp of molecular biology and evolution. By the end, participants can run a basic phylogenetic analysis and know why their result looks the way it does.
Workshop materials
Slides + recording Lecture slides and a video of the full session Two slide formats and a Zoom recording for self-paced review.
The slides cover every topic presented during the workshop, suitable as a primary reference or as a refresher. The recording lets anyone who could not attend live go through the material at their own pace.
Practice datasets
Primate phylogeny Ape dataset, three formats Well-characterized sequences for alignment practice and tree building.
The ape dataset is a well-studied primate phylogeny, ideal for learning sequence alignment and tree building. Results can be verified against known evolutionary relationships. Provided in three formats for compatibility with the major phylogenetics packages.
Scarab beetles A harder problem from Coleoptera Greater evolutionary complexity and diversity than the ape set.
The scarab beetle dataset represents a more complex phylogenetic problem drawn from Coleoptera, one of the most diverse animal groups. It is well suited for applying the techniques from the workshop to a real research dataset and is an excellent warm-up for advanced tree building and assessment approaches.
- FASTA (scarab.fa) standard format for sequence data across multiple platforms.
- NEXUS (scarab.nex) for Bayesian analysis and other NEXUS-compatible software.
Software and tools
Recommended packages Four programs that cover the full workflow From alignment through Bayesian inference to publication-ready figures.
- MEGA (Molecular Evolutionary Genetics Analysis). Comprehensive software for sequence alignment, tree building (neighbor-joining, maximum likelihood), and visualization. A user-friendly entry point.
- FigTree. Tree viewer and editor for annotating and publishing phylogenies. Produces figure-ready output.
- RAxML (Randomized Axelerated Maximum Likelihood). High-performance likelihood inference, handles large datasets, built-in bootstrapping.
- MrBayes. Bayesian phylogenetic inference. Produces posterior probability distributions over trees and parameters.
Start with MEGA if you are new to phylogenetics, since it integrates alignment, tree building, and visualization in one interface. Once you are comfortable, move to RAxML and MrBayes for more advanced analyses.
Contact
Questions Workshop questions and analysis guidance Heath Blackmon, TAMU Biology.
For questions about the workshop, the materials, or for guidance on a phylogenetic analysis, email blackmon@tamu.edu. We welcome questions and are happy to provide additional resources or clarification.