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Open Access Open Badges Research article

Whole genome molecular phylogeny of large dsDNA viruses using composition vector method

Lei Gao12* and Ji Qi3

Author Affiliations

1 The Institute of Theoretical Physics, Academia Sinica, Beijing 100080, China

2 The T-Life Research Center, c/o Department of Physics, Fudan University, Shanghai 200433, China

3 Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA 16802, USA

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BMC Evolutionary Biology 2007, 7:41  doi:10.1186/1471-2148-7-41

Published: 15 March 2007



One important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events. The recent composition vector approach, not sensitive to such events, is applied here to reconstruct the phylogeny of 124 large DNA viruses.


The results are mostly consistent with the biologist's systematics with only a few outliers and can also provide some information for those unclassified viruses and cladistic relationships of several families.


With composition vector approach we obtained the phylogenetic tree of large DNA viruses, which not only give results comparable to biologist's systematics but also provide a new way for recovering the phylogeny of viruses.