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.

Step

O(Space)

O(Time)


Distance matrix

N2 + L

N2L2

Neighbor joining

N2

N4

Progressive (one iteration)

NLP + LP = NL + L2

NLP + LP2 = N2 + L2

Progressive (total)

NL + L2

N3 + NL2

TOTAL

N2 + L2

N4 + L2


Edgar BMC Bioinformatics 2004 5:113   doi:10.1186/1471-2105-5-113

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