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OpenTreeOfLife / germinator

miscellaneous scripts and data for concerns that span more than one of the Open Tree code repositories: integration tests, system statistics, etc.
BSD 2-Clause "Simplified" License
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add taxonomic-vs-phylogenetic distinction to induced_subtree #124

Open arlin opened 7 years ago

arlin commented 7 years ago

The main synthetic-tree view uses dotted lines for edges supported only by taxonomy.

Add an option to induced_subtree to support returning the relevant information, so that clients can distinguish taxonomic and phylogenetic parts of the tree.

Complications

  1. Currently induced_subtree returns Newick so it is impossible to put this in the tree. However, if there were a nexson or arguson option, this could include a designation for each edge. Alternatively, without a new format, phyloreferences could be used in the manner suggested in #125.
  2. This will require a method for assigning the status of an induced edge collapsed from a series of original edges in the full synth tree.