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Table 1 Computation time for each sequence length (1 million sequences)

From: Acceleration of sequence clustering using longest common subsequence filtering

  100 bases 150 bases 400 bases
CD-HIT 41m40s   45m15s   1h4m29s  
LCS-HIT 7m10s (5.8) 13m45s (3.3) 31m22s (2.1)