otc-annotate-synth \
	../opentree5.0/cleaned_ott/cleaned_ott.tre \
	../opentree5.0/labelled_supertree/labelled_supertree.tre \
	$(sed "s:^:../opentree5.0/exemplified_phylo/:" ../opentree5.0/exemplified_phylo/nonempty_trees.txt) \
	> ../opentree5.0/annotated_supertree/preannotations1.json
bin/add_subproblem_info_to_annotations.py \
	../opentree5.0/subproblems/subproblem-ids.txt \
	../opentree5.0/annotated_supertree/preannotations1.json \
	../opentree5.0/annotated_supertree/annotations1.json
bin/gen_attributes.py --config=../opentree5.0/config ../opentree5.0 > ../opentree5.0/annotated_supertree/annotations2.json
bin/merge-json.py \
	../opentree5.0/annotated_supertree/annotations1.json \
	../opentree5.0/annotated_supertree/annotations2.json \
	> ../opentree5.0/annotated_supertree/annotations.json