Average execution times. The total wall clock times for each method to align 3,591 pairs and for the RSE to refine them were recorded on Dual 2 GHz PowerPC G5 with 4GB memory, running Mac OS X version 10.3.9. The pre-processing times for MATRAS and VAST were not included. The x- and y-axes show the methods and the average times in seconds, respectively. The times taken by the methods and by the RSE are shown in black bars and red tips, respectively.