I am using PhyloNet to compute the MAST of two unrooted binary phylogenetic trees but I am not getting the output that I should. I think the issue might be with the way I am writing the trees in the input, but I don't know.

For example: if I input T1=((((1,5),6), (2,4)),3) and T2=((1,2), (((3,5),6),4)), the MAST returned is ((1,2),3), whereas if I draw the trees, I get the MAST ((3,6),(4,2)).

I think this might happen because somehow it assumes a root, but I have no idea how to fix it or if that is really the issue. Any guidelines for computing MASTs of unrooted trees are appreciated.


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