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Table 1 Distance values calculated with our algorithm for a pair of simulated sequences of length \(L=500\) kb with a match rate of \(p=0.5\), corresponding to a distance of 0.824 substitutions per position

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

 

k = 30

k = 50

k = 70

k = 90

k = 120

k = 150

k = 200

w = 1

0.665

0.809

0.935

0.897

0.794

0.781

0.995

w = 5

–

0.839

0.835

0.784

0.783

0.773

0.880

w = 11

–

–

0.869

0.808

0.788

0.781

0.863

w = 21

–

–

0.813

0.824

0.824

0.804

0.817

w = 31

–

–

0.813

0.824

0.824

0.829

0.835

w = 51

–

–

–

–

0.824

0.819

0.820

  1. Dashes indicate that no distance value could be calculated since our algorithm could not find the second local maximum in the smoothed length distribution of the k-mismatch common substrings
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Algorithms for Molecular Biology

ISSN: 1748-7188