The ETE tutorial

Contents:

• Working With Tree Data Structures
  • Trees
  • Reading and Writing Newick Trees
    • Reading newick trees
    • Writing newick trees
  • Understanding ETE Trees
  • Basic tree attributes
    • Root node on unrooted trees?
  • Browsing trees (traversing)
    • Getting Leaves, Descendants and Node’s Relatives
    • Traversing (browsing) trees
    • Advanced traversing (stopping criteria)
    • Iterating instead of Getting
    • Finding nodes by their attributes
  • Checking the monophyly of attributes within a tree
  • Caching tree content for faster lookup operations
  • Node annotation
  • Comparing Trees
    • Calculate distances between trees
    • Robinson-foulds distance
  • Modifying Tree Topology
    • Creating Trees from Scratch
    • Deleting (eliminating) and Removing (detaching) nodes
  • Pruning trees
  • Concatenating trees
  • Copying (duplicating) trees
  • Solving multifurcations
  • Tree Rooting
  • Working with branch distances
    • Getting distances between nodes
    • getting midpoint outgroup
• The Programmable Tree Drawing Engine
  • Overview
  • Interactive visualization of trees
  • Rendering trees as images
  • Customizing the aspect of trees
    • Tree style
    • Node style
    • Node faces
    • layout functions
  • Combining styles, faces and layouts
    • Fixed node styles
    • Node backgrounds
    • Img Faces
    • Bubble tree maps
    • Trees within trees
    • Phylogenetic trees and sequence domains
    • Creating your custom interactive Item faces
• Phylogenetic Trees
  • Overview
  • Linking Phylogenetic Trees with Multiple Sequence Alignments
  • Visualization of phylogenetic trees
  • Adding taxonomic information
    • Automatic control of species info
    • Automatic (and custom) control of the species info
    • Manual control of the species info
  • Detecting evolutionary events
    • Species Overlap (SO) algorithm
    • Tree reconciliation algorithm
    • A closer look to the evolutionary event object
  • Relative dating phylogenetic nodes
    • Implementation
  • Automatic rooting (outgroup detection)
  • Working with duplicated gene families
    • Treeko (splitting gene trees into species trees)
    • Splitting gene trees by duplication events
    • Collapse species specific duplications
• Clustering Trees
  • Overview
  • Loading ClusterTrees
  • Visualization of matrix associated Trees
  • Cluster Validation Example
• Phylogenetic XML standards
  • NeXML
    • Reading NeXML projects
    • NeXML tree manipulation and visualization
  • PhyloXML
    • Loading PhyloXML projects from files
    • Creating PhyloXML projects from scratch
• Interactive web tree visualization
  • NO X system available?
  • Installing a X server
  • Servers
  • Desktops
  • Configuring the web sever
  • Implementation of WebTreeApplications
• Testing Evolutionary Hypothesis
  • Extension Requirements:
  • Overview
    • The working directory
  • Descriptive analysis
    • Branch model
    • Site model
  • Hypothesis Testing
    • Test on sites
    • Test on branches
    • Test on branch-sites
  • Utilities
    • Load precomputed evolutionary model
  • References
• Dealing with the NCBI Taxonomy database
  • Setting up a local copy of the NCBI taxonomy database
  • Upgrading the local database
  • Getting taxid information
  • Getting descendant taxa
  • Getting NCBI species tree topology
  • Automatic tree annotation using NCBI taxonomy
• SCRIPTS: orthoXML
  • OrthoXML parser
  • The etree2orthoxml script
    • Usage
    • Example: Using custom evolutionary annotation
    • Example: Automatic detection of species names
    • Example: Tree rooting