We only have implemented the well-known Zhang algorithm. The result is color on the two trees. If two nodes of two different trees have the same color then it means that Zhang algorithm suggests to map one node into the other. If the color is white then it means that Zhang algorithm does not map this node on any node.
There is no interaction. Below are the view for phylo_A_BAD1_ABC_03-02-01.xml and phylo_A_BAD2_ABC_03-02-01.xml.