Table 5.

Likelihood scores, parameter estimates, ΔAIC and ΔAIC_C scores for genes located in the regions of the Listeria genome encoding putative flagellar related proteins.

		Parameter estimates
Model	ℓ	c	ω	κ	ΔAIC (ΔAICC)
1 (E)	-64965.25	(c1 = 1) c2 = 1.18 c3 = 1.42	ω1 = 0.02 ω2 = 0.03 ω3 = 0.10	κ1 = 1.97 κ2 = 1.59 κ3 = 1.62	22.2 (28.2)
2 (D)	-65076.39	(c1 = 1) c2 = 1.21 c3 = 1.37	ω1 = 0.02 ω2 = 0.04 ω3 = 0.10	κ1 = 1.91 κ2 = 1.76 κ3 = 1.62	0.5 (0.6)
3	-65000.40	(c = 1)	ω1 = 0.02 ω2 = 0.03 ω3 = 0.11	κ1 = 2.02 κ2 = 1.56 κ3 = 1.56	88.5 (94.3)
4	-65107.87	(c = 1)	ω1 = 0.02 ω2 = 0.04 ω3 = 0.11	κ1 = 1.97 κ2 = 1.74 κ3 = 1.57	59.5 (59.5)
5	-65106.46	(c1 = 1) c2 = 1.21 c3 = 1.59	ω = 0.03	κ1 = 2.10 κ2 = 1.54 κ3 = 1.22	300.7 (306.5)
6	-65219.99	(c1 = 1) c2 = 1.25 c3 = 1.51	ω = 0.03	κ1 = 2.06 κ2 = 1.68 κ3 = 1.21	283.7 (283.7)
7	-65162.07	(c = 1)	ω = 0.03	κ1 = 2.18 κ2 = 1.50 κ3 = 1.14	407.9 (413.5)
8	-65269.12	(c = 1)	ω = 0.03	κ1 = 2.14 κ2 = 1.65 κ3 = 1.15	378.0 (377.9)
9	-64969.44	(c1 = 1) c2 = 1.20 c3 = 1.44	ω1 = 0.02 ω2 = 0.04 ω3 = 0.11	κ = 1.86	26.6 (32.4
10	-65078.13	(c1 = 1) c2 = 1.22 c3 = 1.38	ω1 = 0.02 ω2 = 0.04 ω3 = 0.11	κ = 1.85	0 (0)
11	-65007.34	(c = 1)	ω1 = 0.02 ω2 = 0.04 ω3 = 0.12	κ = 1.89	98.4 (104.1)
12	-65111.31	(c = 1)	ω1 = 0.02 ω2 = 0.04 ω3 = 0.11	κ = 1.89	62.4 (62.4)
13 (C)	-65124.90	(c1 = 1) c2 = 1.24 c3 = 1.66	ω = 0.03	κ = 1.83	333.6 (339.2)
14 (B)	-65235.39	(c1 = 1) c2 = 1.27 c3 = 1.57	ω = 0.03	κ = 1.83	310.5 (310.5)
15	-65190.76	(c = 1)	ω = 0.03	κ = 1.81	461.5 (466.8)
16 (A)	-65292.90	(c = 1)	ω = 0.03	κ = 1.83	421.5 (421.4)

Parameters in parentheses are fixed. Partition 1 contained genes known to encode components of the flagellar machinery (7973 codons). Partition 2 contained genes encoding proteins with unknown functions (2308 codons). Partition 3 contained genes encoding proteins with non-flagellar functions (1427 codons). ΔAIC_i = AIC_i - min AIC, and ΔAIC_Ci = AIC_Ci - min AIC_C.