Table 1. Estimated proportions of deleterious, neutral, and advantageous nonsynonymous mutations in simulated data sets when the distribution of fitnesses is unimodal for trees with varying number of taxa.

	n taxa
	128			512			4096
Penalty	p−	p0	p+	p−	p0	p+	p−	p0	p+
True	0.243	0.748	0.009	0.243	0.748	0.009	0.243	0.748	0.009
No penalty (λ = 0)	0.583	0.408	0.008	0.431	0.558	0.011	0.271	0.719	0.010
Normal
σ = 1000	0.584	0.408	0.008	0.431	0.558	0.011	0.271	0.719	0.010
σ = 100	0.583	0.409	0.008	0.430	0.559	0.011	0.271	0.720	0.010
σ = 10	0.560	0.429	0.012	0.418	0.571	0.012	0.270	0.720	0.010
Dirichlet
α = 0.01	0.557	0.433	0.010	0.418	0.571	0.011	0.270	0.721	0.010
α = 0.1	0.378	0.610	0.012	0.344	0.645	0.011	0.261	0.729	0.009
α = 1.0	0.088	0.910	0.002	0.143	0.852	0.004	0.216	0.776	0.008