Organization of the sets of adjacencies considered in Step a). A tree whose nodes represent sets of conserved adjacencies found at the current step of the method, and edges represent the inclusion relations between the sets: the root of the tree is the set S of all conserved adjacencies. Abbreviations: FS (Fully-conserved adjacencies), PS (Partly-conserved adjacencies), NC (Non-Conflicting), C (Conflicting), R (Retained), and D (Discarded). Non-conflicting sets are represented with square nodes. The sets of non-conflicting adjacencies added at the current step are represented with black-colored nodes. The sets of conflicting adjacencies saved for the next step b) are represented with gray-colored nodes.