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Tools for manipulating lists of things, and taxonomic checklists in particular.

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listtools

(Sources on main branch are in a somewhat inconsistent state; Makefile and documentation require revision. )

Tools for manipulating lists of things, and in particular, lists of taxonomic names (i.e. 'checklists'), which are sometimes organized hierachically.

If you're eager to get going, check the example and maybe this cheat sheet.

Note

As is customary in computer science, trees grow downwards, like a root system, not upwards. So:

  • The root is at the top of the tree; we go up the tree to get to the root.
  • As sets of individual specimens/observations, taxa are therefore bigger toward the top/root, and smaller toward the bottom/tips.
  • As an upper semilattice, the root is the top node, and is greater than all others; the tips are smallest. A < B means that A is descended from B.

As is customary in biology, we say 'tip' rather than 'leaf' for generality, in case someone is tempted to take 'leaf' too literally. Oddly, the same is not done for 'root'.

The genesis for this software was a conversation around 2018 or 2019 with Nico Franz, who suggested that a generic tool for comparing checklists might be widely useful. Before this conversation I had been working on smasher (see article), which did something similar, and I felt a desire to rewrite it on a firmer theoretical foundation to make it "more sound", and to create a free-standing tool independent of the Open Tree of Life project or any other framework.

This tool suite replaces the older 'checklist diff' tool.

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