Guohong Albert Wu, Se-Ran Jun, Gregory E. Sims, Sung-Hou Kim. Whole-proteome phylogeny of large dsDNA virus families by an alignment-freemethod. Proceedings of the National Academy of Sciences of the United States of America, 106(31):12826-31. 2009.
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The vast sequence divergence among different virus groups has presented a great challenge to alignment-based sequence comparison among different virus families. Using an alignment-free comparison method, we construct the whole-proteome phylogeny for a population of viruses from 11 viral families comprising 142 large dsDNA eukaryote viruses. The method is based on the feature frequency profiles (FFP), where the length of the feature (l-mer) is selected to be optimal for phylogenomic inference. We observe that (i) the FFP phylogeny segregates the population into clades, the membership of each has remarkable agreement with current classification by the International Committee on the Taxonomy of Viruses, with one exception that the mimivirus joins the phycodnavirus family; (ii) the FFP tree detects potential evolutionary relationships among some viral families; (iii) the relative position of the 3 herpesvirus subfamilies in the FFP tree differs from gene alignment-based analysis; (iv) the FFP tree suggests the taxonomic positions of certain \"unclassified\" viruses; and (v) the FFP method identifies candidates for horizontal gene transfer between virus families.