taxonomy dump containing only taxa present in tree

[snacktavish]

For questions like "suppose someone wants to make a tree of all families using opentree." it would be helpful to have a pruned version of the taxonomy that includes only taxa present in the tree. Do we have that anywhere?

[bredelings]

Yeah... we should have that.

This should be present as the "cleaned ott" from: About >> Latest synthesis release >> Browse the full output >> cleaned_ott/index.html >> "download newick"

[jar398]

Smasher has enough infrastructure that this might be a pretty small python (jython) script. For example, it has code already to read synthetic trees. I think it has code to do subsets ('induced subtree') but I'm not sure.