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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Phylogeny reconstruction based on the length distribution of k-mismatch common substrings
Burkhard Morgenstern1, Svenja Schöbel1, Chris-André Leimeister1
1Department of Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077 Göttingen, Germany.
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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