Tutorial

Contents:

• The Tree structure
  • Trees
  • Reading and writing newick trees
  • Understanding ETE trees
  • Basic tree attributes
  • Browsing trees (traversing)
  • Checking the monophyly of properties within a tree
  • Caching tree content for faster lookup operations
  • Node annotation
  • Comparing trees
  • Modifying tree topology
  • Pruning trees
  • Concatenating trees
  • Copying (duplicating) trees
  • Solving multifurcations
  • Tree rooting
  • Working with branch distances
  • Getting midpoint outgroup
• Phylogenetic trees
  • Overview
  • Linking phylogenetic trees with multiple sequence alignments
  • Visualization of phylogenetic trees
  • Adding taxonomic information
  • Detecting evolutionary events
  • Relative dating of phylogenetic nodes
  • Automatic rooting (outgroup detection)
  • Working with duplicated gene families
• Tree drawing and exploration (web)
  • Overview
  • Using the explorer
  • Customizing the visualization
  • Combining styles and faces
• Tree drawing (Qt)
  • Overview
  • Interactive visualization of trees
  • Rendering trees as images
  • Customizing the aspect of trees
  • Combining styles, faces and layouts
• Taxonomy databases
  • Overview
  • Differences between NCBI and GTDB taxonomies in ETE4
  • Setting up local copies of the NCBI and GTDB taxonomy databases
  • Getting taxid information
  • Getting descendant taxa
  • Getting species tree topology
  • Automatic tree annotation using NCBI/GTDB taxonomy
• Tree matcher
  • A simple example (only topology)
  • A less simple example (with node expressions)
  • Outside variables
  • Examples from the test suite