Table 1. Maximum-likelihood parameters of selection pressures acting on H. pylori hcpG codons.

Model Code	-InL *	Tree length	κŦ	dN/dS	Parameter Estimates	D [d.f.]¶	?2	P-value	Positively selected sites [Reference sequence: HpI49]
M0 (1-ratio)	5242.663	3.2215	4.768	0.325	ω = 0.325	NA	NA	NA	NA
M1a (Nearly Neutral)	5130.388	3.4698	4.867	0.341	p0 = 0.742, ω0 = 0.111; p1 = 0.258, ω1 = 1	NA	NA	NA	NA
M2a (Positive Selection)	5108.087	3.5508	5.228	0.434	p0 = 0.723, ω0 = 0.117; p1 = 0.256, ω1 = 1; [pS] = 0.021, [ωS] = 4.46	M0 vs M2a [3] M1a vs M2a [2]	269.152 44.602	<0.0001<0.0001	28S, 30P, 36S, 58K, 66A, 79L, 262A
M3 (Discrete)	5105.965	3.551	5.125	0.409	p0 = 0.627, ω0 = 0.083; p1 = 0.334, ω1 = 0.674; [pS] = 0.039, [ωS] = 3.365	M0 vs M3 [4] M1a vs M3 [4]	273.396 44.846	<0.0001<0.0001	21G. 28S, 30P, 36S, 58K, 66A, 79L, 221L, 224S, 262A, 313K
M7 (β)	5135.398	3.4751	4.731	0.321	p = 0.323, q = 0.684	NA	NA	NA	NA
M8 (β,ω S >1)	5106.781	3.556	5.096	0.405	p = 0.465, q = 1.159; p0 = 0.961, [pS] = 0.393, [ωS] = 3.334	M7 vs M8 [2]	57.234	<0.0001	21G. 28S, 30P, 36S, 58K, 66A, 79L, 221L, 224S, 262A, 272S, 313K
M8a (β, ωS = 1)	5128.752	3.525	4.659	0.362	p = 1.516, q = 9.983; p0 = 0.733, [pS] = 0.267, ωS = 1	M8a vs M8 [1]	43.942	<0.0001
M1bra	5177.115	3.2376	4.649	NA	Free ω for each lineage	M0 vs M1bra	131.1	<0.002	NA

^*-InL, Log Likelihood Score.

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

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