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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.