PMC:1635699 / 7606-8159 JSONTXT

{"project":"2_test","denotations":[{"id":"17062125-15661851-1688893","span":{"begin":32,"end":34},"obj":"15661851"},{"id":"17062125-15860779-1688894","span":{"begin":100,"end":102},"obj":"15860779"},{"id":"17062125-15034147-1688895","span":{"begin":512,"end":514},"obj":"15034147"},{"id":"17062125-15318951-1688896","span":{"begin":515,"end":517},"obj":"15318951"}],"text":"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."}