Interpreting Phylogenies - Exercises

Aidan Budd

Viewing and Manipulating Unscaled Trees with NJplot

• Notes
• Demonstration
• Exercise

Alignments

• Structure-Based Interpretation of Alignments
• Exampes of Non-Equivalence of Evolutionary and Structural Alignment
• "Manual" Alignments using JalView

Working with Scaled Trees in Dendroscope

• Formating Trees for Figures
• Working with Large Trees

NEWICK/PHYLIP Format

• Notes
• Demonstration
• Exercise

Phylogenetic Analysis - From Start to Finish

• General Notes
• Phylogenies from A-Z with RAxML
• Obtaining an initial alignment
  
• Demonstration
• Exercise
• Refining the alignment (adding/removing/editing sequences)
• Demonstration
• Exercise
• Reduce the alignment
• Demonstration
• Exercise
• Estimate phylogeny
• Demonstration
• Exercise

• Phylogenetic Workflow Using Unrelated Sequences
• Exercise
  

Phylogenetic Splits

• Notes
• Analysing Splits "by hand"
  
• Exercise
• Building Consensus Trees "by hand"
• Exercise
• Building Consensus Trees and Split Networks using CONSENSE and SplitsTree
• Exercise

Editing Trees with MESQUITE

• Notes
  
• Demonstration
• Exercises