Additional file 8.

Best likelihood models and estimates of the proportion of adaptive substitutions across loci (α¯). Divergence was measured to the inferred ancestral sequence of the P. chabaudi-P. vinckei clade (P. c. chabaudi and P. v. subsp.) or the P. berghei-P. yoelii clade (P. y. yoelii). The best (highest Akaike weight) and secondary models are shown, with Akaike weights in brackets. Estimates of α¯ (and 95% CI) across loci were obtained from 1000 bootstraps on the results of model ii. Likelihood models: i) α is constrained to zero at all loci, i.e. no adaptive evolution; ii) α is a free-parameter common to all loci; and iii) α can take a different value at each locus.

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Ramiro et al. BMC Evolutionary Biology 2012 12:219   doi:10.1186/1471-2148-12-219