Esteban and Hutchinson BMC Genomics 2011, 12:261 http://www.biomedcentral.com/1471-2164/12/261 Page 5 of 12 Figure 1 Proportion of sites under diversifying selection in each gene in the CPXV genome . Black: Genes with sites under diversifying selection (Genes for which the alternative model, allowing positively sites with ω > 1, fits the data better than the model (p < 0.05)). White: Genes without sites under diversifying selection. A) Proportions determined using model M2a and LRT against M1a. B) Proportions determined using model M8 and LRT against M7. predicted to be under diversifying selection in IL-18BP, and 7 sites are under diversifying selection in the highly conserved C-terminal domain of the mitochondrial asso- ciated apoptosis inhibitor, and an additional 2 are in the N-terminal region. For other genes, the specific residues with a high posterior probability of falling into the diversifying selection site class are given in Additional file 6 and Additional file 7. Discussion In this study we analyzed a large set of poxvirus genes with the purpose of identifying genes experiencing adap- tive molecular evolution. Of 235 genes in the Cowpox virus genome, 175 were analyzed using phylogenetic analysis of maximum likelihood (PAML) and subse- quently analyzed by Bayes empirical Bayes to determine the probability of each codon falling into the three