The results of reference-independent assessment. Results of reference-independent assessment of structural alignments are plotted on (Nali, RMSD) plane for all the tests (lines to guide the eye). X-axis and y-axis indicate the normalized number of aligned residues and its RMSD, respectively The line color represents program: black(DaliLite), cyan(TM-align), gray(CE), red(MICAN), blue(DEDAL), salmon(SNAP), green(GANGSTA+), orange(SCALI), purple(MASS), and yellow(SAMO), and the line style represents a type of the program: dotted lines represent sequential alignment programs, and normal lines non-sequential alignment programs. The benchmark sets are represented by the symbols: squares(MALIDUP-sq/ns) and circles(MALISAM-sq/ns). (a) and (b) show relationship between Nali and RMSD for sequential and non-sequential test sets, respectively. (c) and (d) show relationship between and RMSD for sequential and non-sequential test sets, respectively.