Table 5. Estimated proportions of deleterious, neutral, and advantageous nonsynonymous mutations in real data sets.

	Data set
	rbcL			Mit proteins			PB2
Penalty	p−	p0	p+	p−	p0	p+	p−	p0	p+
No penalty (λ = 0)	0.952	0.042	0.006	0.893	0.103	0.005	0.948	0.047	0.005
Normal
σ = 100	0.952	0.042	0.006	0.893	0.103	0.005	0.947	0.048	0.005
σ = 10	0.943	0.049	0.007	0.888	0.107	0.005	0.931	0.063	0.006
Dirichlet
α = 0.01	0.939	0.054	0.008	0.875	0.120	0.005	0.894	0.098	0.008
α = 0.1	0.805	0.184	0.010	0.747	0.245	0.008	0.633	0.356	0.011