Figure 4.

Core of the simple GIGA algorithm. OS = orthologous subtree, a portion of the gene tree containing only speciation events; FCE = founding copying event, the event (located relative to speciation events) that founded a given OS; in this first implementation of GIGA all FCEs are duplication events. The algorithm begins with each sequence in its own, separate OS. Each iteration operates on the currently closest pair of OS's. At each iteration, either 1) the two OS's are merged into a single OS (right side), or 2) one (or both) OS's are assigned FCEs. The tree is complete when all OS's have been assigned FCEs.