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Table 3 Alignment time of 4 complete genomes of Streptococcus pyogenes with various settings of MISHIMA

From: MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

Method Alignment time
MISHIMA -max-depth = 1 -aligner = clustalw 10:08:52
MISHIMA -max-depth = 2 -aligner = clustalw 02:54:48
MISHIMA -max-depth = 3 -aligner = clustalw 02:33:44
MISHIMA (unlimited depth) -aligner = clustalw 02:43:03
MISHIMA -max-depth = 1 -align-seeds-only 00:00:27