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. 2009 May 21;58(1):130–145. doi: 10.1093/sysbio/syp017

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FIGURE 1. — Simulation design. Among-site rate variation was simulated using 6 rates of evolution (chosen to produce the desired PP for the true tree with 500 sites) combined across 2 genes to form 36 rate combinations. Gene A contained unambiguous sites, whereas Gene B contained ambiguous sites. Ambiguous characters were present for either sister or nonsister taxa. Although Gene A always contained 500 sites, the length of Gene B varied from 0 to 500 sites. Note that Gene B contained no topological information, regardless of the rate of evolution. PP = posterior probabilities.