I've been thinking about and searching for strategies to combine information of phylogenetic trees. My problem is a little different than what is usually done. Suppose I have 2 phylogenetic trees, constructed from sequences of 2 different loci (each tree from one single locus). I know that the trees were obtained from the same organisms, but I don't know the correspondence between the tips of the trees. That means that the trees can be considered as unlabeled or having different labels.
What I want to figure out, is a way to match tips from one tree with tips from the other tree so that in the end I get as close as possible of having sets of 2 tips each, one from one tree and one from the other that are from the same species, meaning that by comparing the trees in some way I could match sequences from different loci without knowing their order or having a common labeling.
Imagine that this represents the tips of the trees:
species1_locusA species4_locusB species4_locusA species1_locusB species2_locusA species3_locusB species3_locusA species2_locusB
I only know that one tree is from locus A of 4 species and the other tree is from locus B of the same species. They don't have labels or have different labels so I can't match things by labels. Due to tree discordance and use of different loci, the trees won't match in terms of topology but might have some similarities.
Does anyone know a way to start looking into this or know some research that might help? As far as I've seen, most programs need trees with the same labels or a correspondence between labels.
Thanks in advance for any help.