Figure 4

Genome alignment accuracies with 495 combinations of score parameters. Each point represents one genome alignment with one combination of score parameters. A few of these are highlighted with symbols: see the key beneath the figure. True positives (horizontal axis) and false positives (vertical axis) were counted with reference to either Rfam (upper row) or TreeFam (lower row). Colors indicate the X-drop parameter. For black points: the X-drop parameter was set to allow a maximum gap size of 20; red: 30; blue: 50; green: 100 and magenta: 200. The same results, but with different scoring schemes highlighted, are shown in Additional file 1, Figure S2.