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ChriZiegler edited this page Jul 27, 2015 · 6 revisions

Things to document

Purpose and design philosophy

Interactive use

  • IPython shell
  • matplotlib tree figures
  • customizing callbacks
  • highlight nodes
  • interactively drop nodes?
  • collapse selected nodes to polytomy?
  • juxtaposed trees
  • displaying bootstrap values
  • alignment figures
  • performing analyses
  • read in character values
  • perform PICs
  • reconstruct ancestral states
  • phylorate plot
  • BiSSE?
  • LTT plot?
  • Interaction with lagrange?

API

  • tree data structure
  • node traversal
  • modifying a tree? (drop nodes, etc.)
  • make a tree ultrametric?
  • reading and writing trees
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