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Computing Maximum Agreement Subtree of two unrooted phylogenetic trees with PhyloNet?

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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I think you might have clicked on "help with Confluence" instead of "help with the things that are being written about in this Confluence installation"

You'll need to ask the authors of your documentation, not the Atlassian community (us) about this.

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