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Open Access Highly Accessed Research article

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Zu-Guo Yu12, Ka Hou Chu3*, Chi Pang Li3, Vo Anh1, Li-Qian Zhou2 and Roger Wei Wang4

Author Affiliations

1 School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Q 4001, Australia

2 School of Mathematics and Computational Science, Xiangtan University, Hunan 411105, China

3 Department of Biology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China

4 Department of Mathematics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China

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BMC Evolutionary Biology 2010, 10:192  doi:10.1186/1471-2148-10-192

Published: 22 June 2010

Abstract

Background

The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes.

Results

In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV).

Conclusions

The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.