How to handle paired h/l data

[Duncan Ralph]

I wonder if there's a sensible way we could handle merged h/l sequences. For regular phylo methods we can just smash together the h and l sequences before inferring trees. I assume we'd never be able to do something like that with linearham -- I imagine like partis there'd be no way for the hmm to handle two rearrangement regions in one sequence -- but maybe there'd be some way to combine the separately-inferred h and l trees?

I won't be surprised if the answer is 'no', but if it's possible I think it could be worth putting some work into. For instance one situation we'd really want to avoid is where we're looking at the separate [most likely] h and l trees and they're inconsistent. I have no idea how much this happens, but if it did happen now we'd have no idea.