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Proper Distance Metrics for Phylogenetic Analysis Using Complete Genomes without Sequence Alignment
School of Mathematics and Computational Science, Xiangtan University, Hunan 411105, China
School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
Department of Mathematics, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
Department of Biology, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
* Author to whom correspondence should be addressed.
Received: 4 February 2010 / Accepted: 3 March 2010 / Published: 18 March 2010
Abstract: A shortcoming of most correlation distance methods based on the composition vectors without alignment developed for phylogenetic analysis using complete genomes is that the “distances” are not proper distance metrics in the strict mathematical sense. In this paper we propose two new correlation-related distance metrics to replace the old one in our dynamical language approach. Four genome datasets are employed to evaluate the effects of this replacement from a biological point of view. We find that the two proper distance metrics yield trees with the same or similar topologies as/to those using the old “distance” and agree with the tree of life based on 16S rRNA in a majority of the basic branches. Hence the two proper correlation-related distance metrics proposed here improve our dynamical language approach for phylogenetic analysis.
Keywords: phylogenetic analysis; complete genome; composition vector; correlation-related distance metric
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Cite This Article
MDPI and ACS Style
Yu, Z.-G.; Zhan, X.-W.; Han, G.-S.; Wang, R.W.; Anh, V.; Chu, K.H. Proper Distance Metrics for Phylogenetic Analysis Using Complete Genomes without Sequence Alignment. Int. J. Mol. Sci. 2010, 11, 1141-1154.
Yu Z-G, Zhan X-W, Han G-S, Wang RW, Anh V, Chu KH. Proper Distance Metrics for Phylogenetic Analysis Using Complete Genomes without Sequence Alignment. International Journal of Molecular Sciences. 2010; 11(3):1141-1154.
Yu, Zu-Guo; Zhan, Xiao-Wen; Han, Guo-Sheng; Wang, Roger W.; Anh, Vo; Chu, Ka Hou. 2010. "Proper Distance Metrics for Phylogenetic Analysis Using Complete Genomes without Sequence Alignment." Int. J. Mol. Sci. 11, no. 3: 1141-1154.