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Homoplasy prevalence in MERS-CoV and simulated datasets. Bars show the proportion of all polymorphic sites that are homoplasic, split by homoplasy degree as inferred by maximum likelihood, in MERS-CoV and datasets simulated with different degrees of rate heterogeneity in the presence or absence of site-specific constraint in the form of a codon model. Homoplasy degree indicates how many times a given mutation has occurred in excess in the phylogenetic tree.
