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

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Abstract

Background: Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between pairs of input sequences. Haubold et al. (J Comput Biol 16:1487-1500, 2009) showed how the average number of substitutions per position between two DNA sequences can be estimated based on the average length of exact common substrings. Results: In this paper, we study the length distribution of k-mismatch common substrings between two sequences. We show that the number of substitutions per position can be accurately estimated from the position of a local maximum in the length distribution of their k-mismatch common substrings.

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Morgenstern, B., Schöbel, S., & Leimeister, C. A. (2017). Phylogeny reconstruction based on the length distribution of k-mismatch common substrings. Algorithms for Molecular Biology, 12(1). https://doi.org/10.1186/s13015-017-0118-8

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