Table 3.

PAML (codeml): Parameters estimates and log-likelihood values under models of variable ω ratios among sites.

Model	Parametersa	lnL	Sites showing indications of positive selection
M0	ω = 0.40548	−6617.469118	None
M1	p0 = 0.64290, p1 = 0.35710 ω0 = 0, ω1 = 1	−6607.96566	Not allowed
M2	p0 = 0.96461, p1 = 0.00003, p2 = 0.03536 ω0 = 0.25444, ω1 = 1, ω2 = 4.90459	−6604.579083	5, 12, 26, 138, 155, 222, 484, 626, 677, 688, 1263
M3	p0 = 0.93156, p1 = 0.03308, p2 = 0.03536 ω0 = 0.25424, ω1 = 0.25458, ω2 = 4.90450	−6604.578953	5, 12, 26, 138, 155, 222, 484, 626, 677, 688, 1263
M7	p = 0.00986, q = 0.01846	−6608.318528	Not allowed
M8	p0 = 0.91883, p = 0.00675, q = 0.04374, p1 = 0.08117, ω = 2.79061	−6605.852845	5, 12, 14, 20, 26, 27, 52, 54, 68, 138, 145, 153, 155, 190, 218, 221, 222, 231, 235, 263, 344, 417, 439, 484, 561, 583, 626, 658, 670, 677, 688, 776, 791, 879, 936, 1005, 1065, 1071, 1072, 1076, 1099, 1104, 1118, 1152, 1162, 1238, 1259, 1263, 1264, 1272

^aω = d_N/d_S = average over sites; p₀,p₁ and p₂ indicate the proportions of groups 0, 1 and 2 in each model, respectively; ω₀, ω₁ and ω₂ indicate the ω values of groups 0, 1 and 2 in each model, respectively. p and q are beta parameters.