Table 2

Complexity of MUSCLE. Here we show the big-O asymptotic complexity of the elements of MUSCLE 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)


K-mer distance matrix

N2 + L

N2L

UPGMA

N2

N2

Progressive (one iteration)

LP2 = NL + L2

LP2 = N2 + L2

Progressive (root alignment)

NLP = N2 + NL

NLP log N = N2 log N + NL log N

Progressive (N iterations + root)

N2 + NL + L2

N3 + NL2

Refinement (one edge)

NLP + LP2 = N2 + L2

N2LP + LP2 = N3+ L2

Refinement (N edges)

N2 + L2

N4+ NL2

TOTAL

N2 + L2

N4 + NL2


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

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