title: Genome-based phylogeny of dsDNA viruses by a novel alignment-free method.
abstract: Sequence alignment is not directly applicable to whole genome phylogeny since several events such as rearrangements make full length alignments impossible. Here, a novel alignment-free method derived from the standpoint of information theory is proposed and used to construct the whole-genome phylogeny for a population of viruses from 13 viral families comprising 218 dsDNA viruses. The method is based on information correlation (IC) and partial information correlation (PIC). We observe that (i) the IC-PIC tree segregates the population into clades, the membership of each is remarkably consistent with biologist's systematics only with little exceptions; (ii) the IC-PIC tree reveals potential evolutionary relationships among some viral families; and (iii) the IC-PIC tree predicts the taxonomic positions of certain "unclassified" viruses. Our approach provides a new way for recovering the phylogeny of viruses, and has practical applications in developing alignment-free methods for sequence classification.
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Gao
authors.forename: Liaofu
authors.initials: L
authors.lastname: Luo
mesh_terms: D004247:DNA; D004267:DNA Viruses / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D016679:Genome, Viral; D007254:Information Science / Q000379:methods*; D007257:Information Theory; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D004247:DNA