Thanks, Joseph.
Running the otcetera tool otc-check-taxonomic-nodes:
otc-check-taxonomic-nodes -d Life_subprobsv3_synth_29April2015.tre supertree/step_1/taxonomy.tre
finds 23 cases of internal nodes in the tree that appear to be incorrectly labeled. This test compares the set of terminal taxa descending from the taxon in the synthetic tree to the set of terminal tax that are descendants of that taxon in OTT. The test does not check for clades in the synth tree that are unlabeled, but should have a label.
I think that this issue may be related to the unsupported nodes. An inspection of the unsupported nodes that Joseph mentioned (see below for longer output) shows that three come from subproblem ott712383 and one of the tips in that subproblem is the genus Siderastrea ott215891. This is also one of the incorrectly labelled taxa (based on the otc-check-taxonomic-nodes check).
all the best,
Mark
output of otcetera/util/inspect_unsupported.py (which requires a very recent peyotl branch and the subproblems on the local fs):
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