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

Phylogeny reconstruction based on the length distribution of k-mismatch common substrings. Algorithms Mol Biol. 2017;12:27 Authors: Morgenstern B, Schöbel S, Leimeister CA 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. PMID: 29238399 [PubMed]
Source: Algorithms for Molecular Biology : AMB - Category: Molecular Biology Authors: Tags: Algorithms Mol Biol Source Type: research