A '3-taxon tree'

[k-gun12]

I've got transcriptomes from three closely related species A, B and their hybrid C. I'm trying to infer which genes from the hybrid have a closer affinity for A or B. I've seen some pubs do this by constructing 4-taxon constraint trees and use CONSEL or some other tool to read site likelihoods and provide a confidence value for each tree, but I'm stuck with three taxa. Since there is no 'three taxon tree', I'm looking at other measures. I've already run straight-up pairwise nucleotide divergence calculations but I'm looking for something with a statistical relevance.

Thanks!