Phylogeny Exercises

Aidan Budd

Phylogenetic Terminology

• Notes
• Exercises

Common Misconceptions about Phylogenies and Evolution

• Exercise

Viewing and Manipulating Unscaled Trees with NJplot

• Notes on the demonstration and exercises
  
• Demonstration
• Exercise

Writing Your Own Trees

• Tree (NEWICK/PHYLIP format) Data
• Notes
• Demonstration
• Exercises
• Fixing errors in a NEWICK string
• Demonstration
  
• Exercises
  

Working with Scaled Trees in Dendroscope

• Formatting Trees for Figures
• Demonstration
• Exercise
  
• Working with Large Trees
• Demonstration and Exercise
  

Phylogenetic Analysis - From Start to Finish

• General Notes
• Phylogenies from A-Z
• Demonstration - focus on carrying out basic tasks, not on addressing a question
  
• Obtaining an initial alignment
  
• Refining the alignment (adding/removing/editing sequences)
• Reduce the alignment
• Choose a substitution model
  
• Estimate phylogeny
• Demonstration - focus on addressing a question
• Exercise
• Phylogenetic Workflow Using Unrelated Sequences
• Exercise