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.
From: MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Step | O(Space) | O(Time) |
|---|---|---|
K-mer distance matrix | N2 + L | N 2 L |
UPGMA | N 2 | N 2 |
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 | N 4 + NL 2 |
TOTAL | N2 + L2 | N4 + NL2 |