Table 2.

Data Sets from Kosakovsky Pond and Muse (2005) Reanalyzed Using the GB Discrete Rate Distribution

	MG94 × REV IB							MG94 × REV GB
Data	N	L	Log L	AICc	E[β – α]	Pr{β > α}	D	Log L	AICc	E[β – α]	Pr{β > α}	Δ AICc
Sperm lysin	25	134	− 4,340.6	8,832.6	− 0.02	0.34	5	− 4,340.3	8,832.6	0.07	0.37	3.1
Primate COXI	21	510	− 11,985.6	24,095.9	− 0.18	0.013	4	− 11,975.5	24,077.7	− 0.98	0.00	18.2
Drosophila adh	23	254	− 4,583.41	9,300.36	− 0.91	0	3	− 4,0583.57	9,296.58	− 0.90	0	3.8
HIV-1 vif	29	192	− 3,334.37	6,826.98	− 0.24	0.28	5	− 3,331.17	6,828.82	− 0.24	0.22	− 1.9
β-globin	17	144	− 3,649.66	7,409.81	− 0.78	0.06	4	− 3,650.3	7,413.2	− 0.77	0.08	− 3.4
IAV HA	349	329	− 10,891.1	23,227.2	− 0.86	0.12	7	− 10,837.9	23,141.1	− 0.52	0.27	86.0
Camelid VHH	212	96	− 16,382.2	33,672.3	− 0.27	0.37	10	− 16,283.6	33,514.9	− 0.25	0.28	157.4
Encephalitis env	23	500	− 6,752.7	13,638.2	− 0.95	0.02	4	− 6,750.1	13,635	− 0.95	0	3.3
Flavivirus NS5	18	342	− 9,144.33	18,402.9	− 0.65	0.01	4	− 9,109.04	18,333.2	− 0.96	0	69.7
Hepatitis D virus Ag	33	196	− 5,078.3	10,330.9	− 0.56	0.44	5	− 5,074.15	10,330.9	− 0.56	0.30	0.03

NOTE.—The optimal number of rate classes D for the GB model was inferred using the step-up procedure described in this manuscript, whereas the total number of rate classes for the IB (dual model in Kosakovsky Pond and Muse 2005) analog were fixed at 3 synonymous × 3 nonsynonymous = 9. N refers to the number of sequences and L to the number of codons in each alignment. E[β – α] is the mean of the estimated β – α distribution, whereas Pr{β > α} is the cumulative probability of all rate classes with β > α in the respective distribution. ΔAIC_c is computed between the GB model with D rate classes and the 3 × 3 IB model.