Exporting SEED classifications



I am trying to export SEED classifications using Export CSV > SEED Path to Counts, however MEGAN always seems to exclude leaves that are present across multiple subsystems and retains only one leaf per protein family (level 4)

In terms of preserving the library size, this makes sense, but messes up analysis that would want to find differential subsystems, as most of the subsystems would be incomplete. Is there a workaround to export all the leaves from the tree?