Exercises

Aidan Budd

Introducing Pairwise/Multiple Sequence Alignments with JalView (2 sequences per file)

• Demonstration
• Exercise 

Structure-Based Interpretation of Alignments

• Demonstration

Making MSAs is Easy

Viewing and Manipulating Unscaled Trees with NJplot

• Notes
• Demonstration
• Exercise

Working with Scaled Trees in Dendroscope

• Formating Trees for Figures
• Working with Large Trees

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

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