Fig. 4.

The accuracy of alignment of DNA (top row) and protein (bottom row) QSs against the corresponding reference alignment using different alignment methods. The x-axis indicates the length of the fragments aligned and the sub-panels show two of the five query species analyzed. Columns (a)–(c) correspond to trees with branch lengths multiplied by 1.5, 2.0 and 2.5, respectively. The accuracy is measured as the correctness of the site-wise homology inference with respect to the closest human/mouse reference sequence