Phylogeny:AP Caulimoviridae

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Method of phylogenenetic reconstruction

Phylogenetic reconstruction inferred based on the protease protein (AP) product encoded by the pol internal region of the Caulimoviridae family, and on a second non-pol protease-like domain encoded by the ORF7 of three soymoviruses and by the C-terminus of CSVMV-ORF I Cavemovirus (downstream to the MOV region) (highlighted in red). The tree has been realized using MEGA 4.1 (Kumar et al. 2008) and the Neighbor joining (NJ) method of phylogenetic reconstruction (Saitou and Nei 1987) with 100 bootstrap replicates under the conditions: uniform rates among sites and pairwise deletion of gaps.

 




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Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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