Phylogenetics 101

A 3-hour foundational workshop in phylogenetic methods and inference

Workshop Overview

Phylogenetics 101 is designed to expose students to the foundational aspects of phylogenetics, including tree thinking, sequence alignment, phylogenetic inference, and tree assessment. This intensive workshop provides hands-on experience with widely-used methods and software tools essential for modern evolutionary biology.

Throughout this workshop, participants will learn:

  • Tree Thinking: Understanding evolutionary relationships and interpreting phylogenetic trees
  • Sequence Alignment: Methods for aligning DNA and protein sequences for phylogenetic analysis
  • Phylogenetic Inference Methods: Neighbor-Joining, Maximum Likelihood, and Bayesian approaches to building evolutionary trees
  • Tree Assessment: Evaluating tree confidence and robustness through bootstrapping and posterior probabilities
  • Software Application: Practical experience with industry-standard phylogenetics software packages

The workshop is intended for upper-level undergraduates and early graduate students with basic understanding of molecular biology and evolution. By the end of the session, participants will be equipped to perform basic phylogenetic analyses and understand the fundamental principles underlying modern phylogenetic methods.

Workshop Materials

Access the lecture slides and workshop recording below. The lecture slides cover all major topics presented during the workshop, providing a comprehensive overview of phylogenetics principles, methods, and applications.

PDF Lecture Slides

Complete lecture slides in PDF format for easy viewing and annotation.

PPTX Lecture Slides

PowerPoint version for viewing animations and full presentation experience.

Workshop Recording

Access the full recording of the workshop session for review or if you were unable to attend live.

Practice Datasets

The following datasets are provided for hands-on practice during and after the workshop. Each dataset demonstrates different aspects of phylogenetic analysis and can be used with various phylogenetics software packages.

Ape Phylogeny Dataset

The ape dataset represents a well-studied primate phylogeny, making it ideal for learning sequence alignment and phylogenetic tree building. This dataset provides a diverse set of primate sequences that are well-characterized in the literature, allowing you to practice alignment methods and verify your results against known evolutionary relationships.

Available in multiple formats for compatibility with different software packages:

apes.nex
NEXUS format - Commonly used with MrBayes and FigTree. Includes metadata and command blocks.
apes.fas
FASTA format - Standard sequence format compatible with most phylogenetics software including BLAST, MEGA, and RAxML.
apes.phy
PHYLIP format - Compact format used by PHYLIP suite and RAxML for efficient computation.

Scarab Beetle Dataset

The scarab beetle dataset represents a more complex phylogenetic problem drawn from Coleoptera (beetles), one of the most diverse animal groups. This dataset is well-suited for applying the techniques learned in the workshop to a real research dataset with greater evolutionary complexity and diversity. It provides excellent practice for advanced tree building and assessment approaches.

Available in two complementary formats:

scarab.fa
FASTA format - Standard format for sequence data analysis across multiple phylogenetics platforms.
scarab.nex
NEXUS format - For Bayesian analysis and other NEXUS-compatible software.

Software & Tools

The following software packages are commonly used in phylogenetic analysis and are recommended for the types of analyses covered in this workshop:

MEGA (Molecular Evolutionary Genetics Analysis)
Comprehensive software for sequence alignment, tree building (neighbor-joining, maximum likelihood), and tree visualization. User-friendly interface with extensive documentation, ideal for learning phylogenetics.
FigTree
Powerful phylogenetic tree viewer and editor for visualizing and annotating trees. Essential for producing publication-quality phylogenetic figures.
RAxML (Randomized Axelerated Maximum Likelihood)
High-performance software for phylogenetic inference using maximum likelihood. Handles large datasets efficiently and includes built-in support for bootstrapping.
MrBayes
Bayesian phylogenetic inference software. Produces posterior probability distributions for trees and parameters, providing a probabilistic framework for phylogenetic analysis.
Getting Started: Start with MEGA if you are new to phylogenetics, as it offers an intuitive interface and integrates alignment, tree building, and visualization. Once comfortable with the fundamentals, explore RAxML and MrBayes for more advanced analyses.

Contact & Questions

For questions about this workshop, the materials provided, or guidance on phylogenetic analyses, please contact:

Dr. Blackmon
Department of Biology
Texas A&M University

We welcome questions and are happy to provide additional resources or clarification on any aspects of phylogenetics covered in this workshop.