Table 1. The values of log-likelihood (l), d N/d S, and parameter estimates in CODEML analysis of human A(H1N1) Has.
| Model | l | d N/d S | Parameters estimates |
| I- i 1918∼1919 (5 strains) 1 | |||
| M0 (one-ratio) | −806.78 | 0.516 | ω = 0.516 |
| M1a (nearly neutral) | −805.91 | 0.323 | p 0 = 0.677 (p 1 = 0.323), ω0 = 0 (ω1 = 1) |
| M2a (positive selection) | −804.19 | 0.564 | p 0 = 0.963, p 1 = 0 (p 2 = 0.037), ω0 = 0 (ω1 = 1), ω2 = 15.421 |
| M7 (beta) | −805.92 | 0.300 | p = 0.005, q = 0.012 |
| M8a (beta&ω = 1) | −805.91 | 0.323 | p 0 = 0.846 (p 1 = 0.154), p = 0.005, q = 0.020, ωs = 1 |
| M8 (beta&ω>1) | −804.19 | 0.561 | p 0 = 0.963 (p 1 = 0.037), p = 0.005, q = 7.228, ωs = 15.242 |
| I- ii 1979∼2000 (45 strains)2 | |||
| M0 (one-ratio) | −2489.23 | 0.223 | ω = 0.223 |
| M1a (nearly neutral) | −2486.25 | 0.242 | p 0 = 0.855 (p 1 = 0.145), ω0 = 0.113 (ω1 = 1) |
| M2a (positive selection) | −2486.25 | 0.242 | p 0 = 0.855, p 1 = 0.056 (p 2 = 0.089), ω0 = 0.113 (ω1 = 1), ω2 = 1 |
| M7 (beta) | −2485.63 | 0.232 | p = 0.327, q = 1.074 |
| M8a (beta&ω = 1) | −2485.63 | 0.232 | p 0 = 1 (p 1 = 0), p = 0.327, q = 1.074, ωs = 1 |
| M8 (beta&ω>1) | −2485.63 | 0.232 | p 0 = 1 (p 1 = 0), p = 0.327, q = 1.074, ωs = 1 |
| I- iii 2000∼2001 (22 strains)2 | |||
| M0 (one-ratio) | −1686.21 | 0.279 | ω = 0.279 |
| M1a (nearly neutral) | −1684.58 | 0.261 | p 0 = 0.793 (p 1 = 0.207), ω0 = 0.068 (ω1 = 1) |
| M2a (positive selection) | −1683.09 | 0.287 | p 0 = 0.994, p 1 = 0 (p 2 = 0.006), ω0 = 0.225 (ω1 = 1), ω2 = 10.636 |
| M7 (beta) | −1684.52 | 0.265 | p = 0.046, q = 0.127 |
| M8a (beta&ω = 1) | −1684.58 | 0.261 | p 0 = 0.793 (p 1 = 0.207), p = 7.211, q = 98.93, ωs = 1 |
| M8 (beta&ω>1) | −1683.10 | 0.287 | p 0 = 0.994 (p 1 = 0.006), p = 28.774, q = 99, ωs = 10.638 |
| I- iv 2001∼2007 (89 strains)2 | |||
| M0 (one-ratio) | −2720.83 | 0.187 | ω = 0.187 |
| M1a (nearly neutral) | −2709.20 | 0.181 | p 0 = 0.883 (p 1 = 0.117), ω0 = 0.072 (ω1 = 1) |
| M2a (positive selection) | −2708.27 | 0.187 | p 0 = 0.906, p 1 = 0.076 (p 2 = 0.018), ω0 = 0.085 (ω1 = 1), ω2 = 1.915 |
| M7 (beta) | −2708.99 | 0.183 | p = 0.137, q = 0.612 |
| M8a (beta&ω = 1) | −2709.40 | 0.180 | p 0 = 0.885 (p 1 = 0.115), p = 7.871, q = 98.995, ωs = 1 |
| M8 (beta&ω>1) | −2708.82 | 0.186 | p 0 = 0.973 (p 1 = 0.027), p = 0.375, q = 2.298, ωs = 1.936 |
| I- v 2006∼2008 (100 strains)2 | |||
| M0 (one-ratio) | −3871.33 | 0.303 | ω = 0.303 |
| M1a (nearly neutral) | −3813.28 | 0.241 | p 0 = 0.828 (p 1 = 0.172), ω0 = 0.082 (ω1 = 1) |
| M2a (positive selection) | −3782.07 | 0.313 | p 0 = 0.807, p 1 = 0.188 (p 2 = 0.005), ω0 = 0.083 (ω1 = 1), ω2 = 11.142 |
| M7 (beta) | −3814.21 | 0.246 | p = 0.139, q = 0.427 |
| M8a (beta&ω = 1) | −3812.40 | 0.231 | p 0 = 0.862 (p 1 = 0.138), p = 0.497, q = 3.969, ωs = 1 |
| M8 (beta&ω>1) | −3781.55 | 0.305 | p 0 = 0.994 (p 1 = 0.006), p = 0.180, q = 0.546, ωs = 10.554 |
| II 2007∼2009 (74 strains)2 | |||
| M0 (one-ratio) | −2374.98 | 0.277 | ω = 0.277 |
| M1a (nearly neutral) | −2373.20 | 0.282 | p 0 = 0.922 (p 1 = 0.078), ω0 = 0.222 (ω1 = 1) |
| M2a (positive selection) | −2372.81 | 0.282 | p 0 = 0.922, p 1 = 0.035 (p 2 = 0.042), ω0 = 0.222 (ω1 = 1), ω2 = 1 |
| M7 (beta) | −2373.21 | 0.281 | p = 1.218, q = 3.079 |
| M8a (beta&ω = 1) | −2374.03 | 0.282 | p 0 = 0.945 (p 1 = 0.055), p = 3.243, q = 10.201, ωs = 1 |
| M8 (beta&ω>1) | −2372.81 | 0.282 | p 0 = 0.946 (p 1 = 0.054), p = 3.158, q = 9.900, ωs = 1 |
1
Due to the inclusion of two partial sequences of A/London/1/1918 and A/London/1/1919 in this subgroup, the analysis was performed on a total of 187 amino-acid residues that covered the antigenic and receptor-binding sites in the region of HA1 (51∼237) [11]. 2 The analysis was performed on the first 340 residues of HA1 including the signal peptide.