Figure 2

(i) An optimal sorting sequence in the general DCJ-indel model - many circular chromosomes can coexist in the intermediate species. (ii) An optimal sorting sequence in the restricted DCJ-indel model - a circular chromosome is immediately reincorporated after its excision. Although the number of steps in (i) and (ii) is the same, the question whether the distance is the same for both general and restricted DCJ-indel models is open. (The common content of the initial and the final genomes is represented in black, while the content exclusive to the initial genome is represented in red.).