Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model |
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| Authors: | Zu-Guo Yu Ka Hou Chu Chi Pang Li Vo Anh Li-Qian Zhou Roger Wei Wang |
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| Institution: | (1) School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Q 4001 Brisbane, Australia;(2) School of Mathematics and Computational Science, Xiangtan University, 411105 Hunan, 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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| 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. |
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