I have around 50 unrotoed phylogenetic trees that are generated using FastTree from 51 different gene families coming from different number of species. Not all of my trees have the same number of leaf nodes. Some might have a few more some a few less.
I want to combine these trees into one consensus (the best one explaining all of them) and also while I do that I would also like to know which leaves of these trees are being mapped (matched) together. I have checked PAUP turns out its not free, I've been trying to work with mesquite but their wiki page is down and website is not being supported. Does anyone have any suggestions of how can I do this?
If let's say a leaf node is not present on one of the trees but present in the other I would like that leaf node to also be present in the final supertree.
Any advice would be appreciated. Thanks.