The fraction of correctly aligned residues ( f
) of each alignment and for each method. The superfamilies along the x-axis were sorted in descending order of the number of alignments in each. The boundaries of those with 50 or more alignments are marked by red vertical lines. The alignments in each superfamily were sorted in ascending order of fcar(0), which are shown in black circles. The grey vertical lines cover the range between fcar(8) and fcar(0) for each alignment. The methods are given in alphabetical order. Note that the order of superfamilies along the x-axis is preserved for all methods, but the order of the individual alignments within a superfamily is not since they are sorted by fcar(0) values, which are specific for each method. Superfamilies marked by the red boundary bars are, from left: cd00096, cd02156, cd01983, cd00900, cd00657, cd02019, cd03440, cd01292, cd02688, cd00314, cd00196, cd00650b, cd00650a, cd00768, cd02184, and cd00267. The bold-faced superfamilies are three of the five exceptional ones identified in Figure 11 and listed in Table 2. These are those for which the fcar(0) values are low (longest grey lines) for all methods.