Inferred numbers of substitutions for each pair of nucleotides as determined through reconstructing ancestral sequences under the non-reversible (12 rate) maximum likelihood model. Sizes of circles are proportional to relative nucleotide substitution rates, whereas counts are inferred numbers of substitutions along the phylogeny, given the maximum likelihood model (expressed as a percentage of the total number of inferred mutations). Counts were used for Chi-square tests (described in methods). Given the expectation that all mutation types are equally likely, circles are colored blue when the mutations they represent are neither more nor less common than expected, red when they are less common than expected and green when they are more common than expected. The hatched circles indicates that although transitions and transversions are are respectively more or less common than would be expected if all mutation types were equally probable, if one only considers the frequencies of transitions in relation to other transitions and transversions in relation to other transversions, then these, mutations are no more or less common than expected.
Harkins et al. Virology Journal 2009 6:104 doi:10.1186/1743-422X-6-104