PMC:1635699 / 10276-11169 JSONTXT

{"project":"2_test","denotations":[{"id":"17062125-16000407-1688899","span":{"begin":68,"end":70},"obj":"16000407"}],"text":"Similarly we optimized gap values for the recently published PRANK [29]. Average ranks can be found in Table 3. Default values (go = 0.025 and ge = 0.5) are too high. Due to time reasons we did not test all parameter combinations; optimal values found so far are 10 times lower than the default values. One should bear in mind that Friedman rank tests do not indicate to which degree a particular program or option works better, but that it consistently performs better. The actual performance gain can be visualized by plotting BRALISCORE vs. reference APSI (see Figure 1). For MAFFT the new options result in an extreme performance gain whereas CLUSTALW gap parameter optimization only yields a modest improvement indicating that CLUSTALW default options are already near optimal. In both cases the influence of optimized parameters has its greatest impact at sequence identities ≤ 55% APSI."}