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Fig. 5 | Algorithms for Molecular Biology

Fig. 5

From: Phylogeny reconstruction based on the length distribution of k-mismatch common substrings

Fig. 5

Theoretical length distribution of k-mismatch common substring extensions. The expected number of k-mismatch extensions of length m returned by kmacs was calculated using Eq. (17), distinguishing between ‘homologous’ and ‘background’ matches, for a pair of sequences of length \(L=500\) kb with a match probability of \(p=0.5\) for \(k=10\) (top) and \(k=70\) (bottom) for \(20\le m \le 160\). A large enough value of k is necessary to detect the second peak in the distribution that corresponds to the ‘homologous’ matches

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