Hey @karen_cranston and @blackrim --
Are there any efforts to prove statistical consistency of the methods that y'all use to build the OTOL? I'm thinking of analogs of papers like @mathmomike and @tandy's few logs paper and the work of Degnan and Rosenberg and many others concerning species tree inference. There are some interesting and perhaps relevant observations in the ML supertrees paper by Steel and Rodrigo.
You would need some random process that would generate observed trees from the true TOL. Not sure what that would be exactly.
For those who don't know about the OTOL methods, here's @blackrim's phyloseminar: