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The plot of sum-of-pairs score (8) versus the average distance of input sequences for five methods, FFT-NS-1, FFT-NS-2, FFT-NS-i, NW-NS-1 and NW-NS-2. The number of input sequences is 40, and sequence lengths are 200 sites on average. Vertical lines indicate the standard deviations of the scores. For all cases, default parameters were used.
