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In early 2016 we retired most of the code that was in this repository and the synthesis method that it implemented. What remains is 'tm-lite' which is described here.

That means that most of the material in this wiki is out of date, as it was prepared when the previous method was current.

For general information about Open Tree of Life, see here.

Tutorials for running treemachine

• Just loading trees, so no additional taxonomy to load.
• [Loading taxonomy] (https://github.com/OpenTreeOfLife/treemachine/wiki/Loading-taxonomy)
• [Loading trees] (https://github.com/OpenTreeOfLife/treemachine/wiki/Loading-trees)
• [Running synthesis] (https://github.com/OpenTreeOfLife/treemachine/wiki/Running-synthesis)

Information for programming with treemachine

• Controlled vocabulary
• NexSON vocabulary can be found here. You can also take a look at this page.
• Vocabulary for the JSON expected by argus is found on the JSON and the Argus-notes document.

Code tutorials

• Methods for graph synthesis

Theory

• This page on the maximum weight of input tree edges displayed with no unsupported edges provides one way to think about the ranked source tree form of synthesis.
• This page on ranked synthesis without the requirement of the TAG.