Current Bioinformatics

Alessandro Giuliani
Istituto Superiore di Sanitá (Italian NIH) Environment and Health Dept
Roma
Italy

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Dissimilarities in Alignment-Free Methods for Phylogenetic Analysis Based on Genomes

Author(s): Xiao-Su Chen, Zu-Guo Yu and Juan Zheng

Affiliation: School of Mathematics and Computational Science, Xiangtan University, Hunan 411105, China.

Keywords: Alignment-free method, dissimilarity, distance, genome, phylogenetic analysis.

Abstract:

Whole genome sequences are generally accepted as excellent tools for studying evolutionary relationships. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignments could not be directly applied to the whole-genome comparison and phylogenomic studies. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. The “distances” used in these alignment-free methods are not proper distance metrics in the strict mathematical sense. In this study, we first review them in a more general frame — dissimilarity. Then we propose some new dissimilarities for phylogenetic analysis. Last three genome datasets are employed to evaluate these dissimilarities from a biological point of view.

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Article Details

VOLUME: 9
ISSUE: 3
Page: [218 - 227]
Pages: 10
DOI: 10.2174/1574893609999140523124702