Parameters for MAFFT version 5 [25] have been optimized by K. Katoh using BRAliBase II's data-set1 [22]. The gap-cost values of MAFFT version 4 (gap-open penalty op = 0.51 and gap-extension penalty ep = 0.041) turned out to be far too low. Applying the improved values (op = 1.53 and ep = 0.123; these are the default in versions ≥ 5.667) to the new BRAliBase 2.1 datasets results in a dramatic performance gain (exemplified in Figure 1 for alignment sets with five sequences). Similarly, parameters for MUSCLE [16,26] have been optimized by its author.