Table 2. Estimated proportions of deleterious, neutral, and advantageous nonsynonymous mutations in simulated data sets when the distribution of fitnesses is bimodal for trees with varying number of taxa.

	n taxa
	128			512			4096
Penalty	p−	p0	p+	p−	p0	p+	p−	p0	p+
True	0.598	0.397	0.004	0.598	0.397	0.004	0.598	0.397	0.004
No penalty (λ = 0)	0.744	0.252	0.004	0.685	0.311	0.005	0.625	0.370	0.005
Normal
σ = 1000	0.744	0.253	0.004	0.685	0.310	0.005	0.625	0.370	0.005
σ = 100	0.743	0.253	0.004	0.685	0.311	0.005	0.625	0.370	0.005
σ = 10	0.729	0.264	0.007	0.677	0.317	0.006	0.622	0.373	0.005
Dirichlet
α = 0.01	0.721	0.272	0.007	0.676	0.319	0.006	0.622	0.373	0.005
α = 0.1	0.545	0.443	0.012	0.598	0.393	0.009	0.607	0.388	0.005
α = 1.0	0.191	0.802	0.007	0.376	0.613	0.011	0.545	0.448	0.007