Figure 1.

Number of cyclic orderings of a set 10 complete mitochondrial genomes with a prescribed fraction of "noisy" characters, i.e., q(C, χ) ≤ 0.8). The cyclic orderings computed by NeighborNet or QNet indeed essentially minimize the fraction of putative randomized alignment sites. At least in this example, QNet with quartet-mapping-derived quartet weights performs best. "ClustalW" refers to the circular ordering implicitly constructed by ClustalW from its guide tree which determines the order in which sequences and profiles are combined to yield the final alignment.