Comparison of performance of DEDAL and other methods on the SISY and RIPC datasets. The quality with which the reference alignments in the (a) SISY, and (b) RIPC sets (see text) are reproduced by DEDAL and other methods. Box-and-whisker distribution plots (see legend to Figure 6) of the agreement with the reference alignments are shown for each method. DEDAL results are shown for both the TS+CTS and CTS+CTS regimes, including scores for the first and best of the five calculated alignments, as well as for the best of both methods. All other results are from Mayr et al. For numerical results see Additional files 8 and 9. On the SISY set, the performance of DEDAL (76% average accuracy, 89% median accuracy) is comparable with that of DALI (76%, and 91% respectively). The third ranked MATRAS achieves 68% average accuracy (88% median). On the more challenging RIPC set, DEDAL significantly outperforms other methods (see also Tables 1 and 2 for the analysis of significance).