title: Estimating evolutionary distances between genomic sequences from spaced-word matches.
abstract: Alignment-free methods are increasingly used to calculate evolutionary distances between DNA and protein sequences as a basis of phylogeny reconstruction. Most of these methods, however, use heuristic distance functions that are not based on any explicit model of molecular evolution. Herein, we propose a simple estimator d N of the evolutionary distance between two DNA sequences that is calculated from the number N of (spaced) word matches between them. We show that this distance function is more accurate than other distance measures that are used by alignment-free methods. In addition, we calculate the variance of the normalized number N of (spaced) word matches. We show that the variance of N is smaller for spaced words than for contiguous words, and that the variance is further reduced if our spaced-words approach is used with multiple patterns of 'match positions' and 'don't care positions'. Our software is available online and as downloadable source code at: http://spaced.gobics.de/.
authors: University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, Göttingen, 37073 Germany ; Université d'Evry Val d'Essonne, Laboratoire Statistique et Génome, UMR CNRS 8071, USC INRA 23 Boulevard de France, Evry, 91037 France.
authors: Burkhard
authors: B
authors: Morgenstern
authors: University of Göttingen, Department of General Microbiology, Grisebachstr. 8, Göttingen, 37073 Germany.
authors: Bingyao
authors: B
authors: Zhu
authors: University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, Göttingen, 37073 Germany.
authors: Sebastian
authors: S
authors: Horwege
authors: University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, Göttingen, 37073 Germany.
authors: Chris André
authors: CA
authors: Leimeister
keywords: Alignment-free; Distance estimation; Genome comparison; Phylogeny; Spaced words; Variance; Word frequency; k-mers