I have 60 marker genes and each gene have different number of species with different species overlapping with each other I want to build a consensus Tree from these trees, I tried using the consense function from PHYLIP tools however the program kept giving errors, I think it did not like the fact that the trees not only had different topologies but also had different number of leaves.
My question is, is it even possible to construct a consensus tree using trees with different sets of leaves with some overlap? Or does constructing a consensus tree by defintion require the trees to have the same number of leaves across?
If so is there any program that does that?
Thank you for your time!