Figure 3
From: Scoredist: A simple and robust protein sequence distance estimator
Estimation of the calibration factor c in Scoredist. This factor rescales the raw distance d r to optimally fit true evolutionary distances. The plot shows how c is estimated by least-squares fitting of raw distances d r to true distances for 2000 artificially produced sequence alignments, using the Dayhoff matrix series. The linear relationship between the raw distance d r and the true distance of the sequence samples justifies the introduction of the calibration factor c, which was here determined to c Dayhoff = 1.3370 (See Table 2).