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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