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

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).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.Viruses were traditionally characterized by morphological features (capsid size, shape, structure, etc) and physicochemical and antigenic properties [1]. At the DNA level, the evolutionary relationships of many families and genera have been explored by sequence analysis of single gene or gene families, such as polymerase, capsid and movement genes [1]. The International Committee on the Taxonomy of Viruses (ICTV) publishes a report on the virus taxonomy system every five years. Phylogenetic and taxonomic studies of viruses based on complete genome data have become increasingly important as more and more whole viral genomes are sequenced [2-6]The phylogeny based on single genes or gene families contains ambiguity because horizontal gene transfer (HGT), along with gene duplication and gene capture from hosts, appear to be frequent in large DNA viruses [7-10]. Whether single-gene based analysis can properly infer viral species phylogeny is debatable [2]. One of the unusual aspects of viral genomes is that they exhibit high sequence divergence [7,11]. Several works have attempted to infer viral phylogeny from their whole genomes [1,2,4,8,12-19]. Among these studies of genome trees, the alignment-free met