I have a set of 13 study subjects from whom I sequenced groups of clones from each of 12 cellular populations.  I would like to test which populations are compartmentalized from which.  Can anyone suggest a way of doing this efficiently?

As it is now, I need to make a separate tree for each pair of populations (12 + 11 + 10 ... + 1 = 78 trees) from each donor (x 13 = 1014 trees) and then test each one separately in HyPhy.

I hope there is an easier way to perform this screening!

Eli