Introduction to Phylogenetics

Contents

• Reasons for making a phylogenetic tree
  • Molecular phylogenetics
• Phylogenetic pipeline
• Building a tree in one click
• Obtaining sequences
  • Orthologues vs. paralogues
  • DNA or protein ?
• Aligning your sequences
  • Methods
    • Progressive sequence alignment
    • Iterative methods
  • Multi-domains proteins
  • Low-complexity regions
• Editing the alignment with Aliview
  • Introduction
    • Start aliview
    • Exercises
• Introduction to distance methods
  • Constructing a phylogenetic tree of primates
    • Introduction
    • Exercise
    • Completed tables from exercise
    • Questions
    • Answers
  • Distance correction methods
• Building trees
  • Introduction
  • File formats
• Phylogenetic Course: Exercises
  • 1. Distance Based Method
  • 2. Parsimony Tree
  • 3. Calculating Maximum Likelihood Trees with RAxML
  • Calculating Bootstrapping Values with RAxML
  • Make ML tree from 10 runs starting with a different parsimony tree
    • Making 5 ML trees each starting from a different parsimonious tree will make max 10 runs on each
  • Drawing Bootstrap trees
  • Tree manipulations
  • Reference and Acknowledgements
  • Further Exercises
    • We pick a workflow name from the list of many from ete3 website and run it:
• Slides and example files
  • Presentation slides
  • Example files
• Links
• References
  • Reading / Hands-on
  • Software
    • Multiple Alignment and Editing
    • Tree visualisation
• Glossary
  • Homology
  • Homoplasy
  • Monophyly
  • Paraphyly
  • Polyphyly
  • Orthologs
  • Paralogs
  • In-paralogs
  • Out-paralogs