Dissimilarities in alignment-free methods for phylogenetic analysis based on genomes

Chen, Xiao-Su, Yu, Zuguo, & Zheng, Juan (2014) Dissimilarities in alignment-free methods for phylogenetic analysis based on genomes. Current Bioinformatics, 9(3), pp. 218-227.

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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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ID Code: 88579
Item Type: Journal Article
Refereed: Yes
Keywords: Alignment-free method, dissimilarity, distance, genome, phylogenetic analysis.
DOI: 10.2174/1574893609999140523124702
ISSN: 1574-8936
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Deposited On: 08 Nov 2015 23:47
Last Modified: 08 Nov 2015 23:47

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