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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. |
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| Step |
O(Space) |
O(Time) |
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| 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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