Figure 2.

Refinement procedure One step of the refinement procedure. Rectangles denote multigenes which belong to non-anchors in the current stage. Rhombus denotes a multigene which is already in an anchor at this stage. Edges connecting rectangles (dashed and solid) are edges of the graph of the current stage. Edges connecting rhombuses are the anchor edges. ‘YES’ means that the edge is keep for the next stage, while ‘NO’ means it is omitted. Parts a) and b) illustrate two situations when we can select one of the edges and leaving out the other. Part c) illustrates the situation when we cannot make such a decision, leading to an unresolved cluster. Both edges are kept in the graph of the next stage. Such a cluster may be resolved at a later stage. Other cases which lead to omitting the edges are possible too.