The software package R [48] offers numerous methods for statistical and graphical data interpretations. We used R version 2.2.0 to carry out the statistical analyses and visualizations of program performances. For a given APSI value, the scores of the alignments are distributed over a wide range (see for example, in Figure 3 the BRALISCOREs range from 0.0 to 1.2 at APSI = 0.45). Furthermore, the alignments are not evenly spaced on the APSI axis. Thus we used the non-parametric lowess function (locally weighted scatter plot smooth) of R to fit a curve through the data points. The lowess function is a locally weighted linear regression, which also takes into consideration horizontally neighbouring values to smooth a data point. The range in which data points are considered is defined by the smoothing factor. The curve in Figure 3 was computed by a smoothing factor of 0.3, which means that a range of 30 % of all data points surrounding the value to smooth are involved.