User’s Guide

ivy is designed to be used both as a library and interactively, in the IPython shell. IPython is an enhanced Python interpreter designed for interactive and exploratory scientific computing.

This screencast demonstrates some basic concepts:

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• 1. Quickstart
  • 1.1. Starting the shell
  • 1.2. Viewing a tree
• 2. Trees in ivy
  • 2.1. Reading
  • 2.2. Viewing
  • 2.3. Navigating
  • 2.4. Testing
  • 2.5. Modifying
    • 2.5.1. Removing
    • 2.5.2. Adding
    • 2.5.3. Ladderizing
    • 2.5.4. Rerooting
    • 2.5.5. Dropping Tips
  • 2.6. Writing
• 3. Using Treebase
  • 3.1. Fetching the study
  • 3.2. Accessing the tree
• 4. Plotting
  • 4.1. Small Trees
  • 4.2. Large Trees
• 5. Analyses
  • 5.1. Phylogenetically Independent Contrasts
  • 5.2. Lineages Through Time
  • 5.3. Phylorate plot
  • 5.4. Mk models
    • 5.4.1. Maximum Likelihood
    • 5.4.2. Bayesian
  • 5.5. Hidden-Rates Models
    • 5.5.1. Maximum Likelihood
  • 5.6. BAMM-like Mk model
  • 5.7. Classe
    • 5.7.1. Maximum likelihood ClaSSE
    • 5.7.2. Maximum likelihood GeoSSE
    • 5.7.3. Creating the pidx array
    • 5.7.4. Creating a likelihood function