The point of making trees is almost always to understand the fundamental sources of phenotypic diversity and making simple models that explain how the new (comp

The point of making trees is almost always to understand the fundamental sources of phenotypic diversity and making simple models that explain how the new (complex, organismal) phenotypes arise, how they are shared through various forms of reproduction and gene transfer, and how those relate to molecular phenotypes. Nobody that I am aware of is clustering things based on similar functionality simply to say "look, these two things are similar", without having some sort of "explanation".