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Running time of the different methods in O notation.
| Running time in O notation | |
|---|---|
| D2 | O(nl+n24k) |
| D2z | (Kantorovitz et al., 2007) |
| D2* | O(n2(l+4k+4m)) |
| N2 | O(n(l+4m+4kNeighbourhoodSize2)+n24k) |
n: number of sequences; l: average sequence length; k:k-mer size; m: Markov model order. The running time for D2*is dominated by the quadratic term. The running time for N2 is dominated by the linear term (pre-processing).
