Table 2. Maximum-likelihood parameters of selection pressures acting on H. pylori hcpC codons.

Model Code	-InL *	Tree length	κŦ	dN/dS	Parameter Estimates	D [d.f.]¶	?2		P-value	Positively selected sites [Reference sequence: HpSh30]
M0 (1-ratio)	6431.304	3.358	3.448	0.1311	ω = 0.1311	NA	NA		NA	NA
M1a (Nearly Neutral)	6137.837	3.447	3.478	0.135	p0 = 0.881, ω0 = 0.018; p1 = 0.119, ω1 = 1	NA		NA	NA	NA
M2a (Positive Selection)	6127.888	3.499	3.82	0.171	p0 = 0.878, ω0 = 0.018; p1 = 0.102, ω1 = 1; [pS] = 0.019, [ωS] = 2.73	M0 vs M2a [3] M1a vs M2a [2]		606.832 19.898	<0.0001<0.0001	9L, 43Q, 75Q, 161T, 229M, 248V
M3 (Discrete)	6124.796	3.483	3.695	0.155	p0 = 0.794, ω0 = 0.004; p1 = 0.119, ω1 = 0.258; [pS] = 0.085, [ωS] = 1.4	M0 vs M3 [4] M1a vs M3 [4]		613.016 26.082	<0.0001<0.0001	3E. 8S, 9L, 17A, 32L, 43Q, 46T, 75Q. 86S, 89A, 95D, 161T, 176A, 192G, 210D, 212V. 213A, 229M, 230Q, 248V, 249T, 273L, 281A
M7 (β)	6131.577	3.389	3.452	0.117	p = 0.021, q = 0.145	NA		NA	NA	NA
M8 (β,ω S >1)	6120.872	3.547	3.742	0.162	p = 0.045, q = 0.375; p0 = 0.978 [pS] = 0.022, [ωS] = 2.51	M7 vs M8 [2]		21.41	<0.0001	8S, 9L, 17A, 43Q, 46T, 75Q, 86S, 89A, 95D, 161T, 176A, 192G, 210D, 212V, 213A, 229M, 230Q, 248V, 249T, 281A
M8a (β, ωS = 1)	6129.478	3.464	3.426	0.127	p = 0.102, q = 3.291; p0 = 0.895, [pS] = 0.104, ωS = 1	M8a vs M8 [1]		17.212	<0.0001	NA
M1bra	6324.72	3.362	3.458	NA	Free ω for each lineage	M0 vs M1bra		213.168	<0.004	NA

^*-InL, Log Likelihood Score.

^∓κ, kappa, ratio of transition to transversions.

^¶D, hierarchical Likelihood Ratio Test statistic and d.f., degrees of freedom.