Honor levels in multi-hierarchy tree alignment?

Question

Good day. I am trying to autoalign a tree with 3 hierarchies. Some of the leaves are also connected to other leaves of a different hierarchy.

 

I there a way to tell the optimizer to honor the hierarchy level? In the attached imaged I indicated what I would expect.

Thanks!

 

Answer 1

Change "Layer Assignment Policy" to "Hierarchical Optimal", enable "Arrows define Edge Direction", and ensure that the edges that connect leaves to other leaves have no arrows and all other edges have arrows at their target ends.