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Table 1 Complexity of CLUSTALW. Here we show the big-O asymptotic complexity of the elements of CLUSTALW as a function of L, the typical sequence length, and N, the number of sequences, retaining the highest-order terms in N with L fixed and vice versa.

From: MUSCLE: a multiple sequence alignment method with reduced time and space complexity

Step O(Space) O(Time)
Distance matrix N2 + L N 2 L 2
Neighbor joining N 2 N 4
Progressive (one iteration) NLP + LP = NL + L2 NLP + LP2 = N2 + L2
Progressive (total) NL + L2 N3 + NL2
TOTAL N2 + L2 N4 + L2