Model | np | â„“ | Parameters | Positively selected sites |
---|---|---|---|---|
M0: One ratio | 137 | -5654.77 | ω= 0.173 | None |
M1a: Nearly neutral | 138 | -5539.34 | p 0 = 0.885, ω 0 = 0.062; p 1 = 0.114, ω 1 = 1 | Not allowed |
M2a: Positive selection | 140 | -5529.73 | p 0 = 0.892, ω 0 = 0.07; p 0 = 0.085, ω 1 = 1; p 2 = 0.023, ω 2 = 2.92 | K30Q |
M3: Discrete | 139 | -5536.84 | p 0 = 0.92, ω 0 = 0.08; p 1 = 0.079, ω 1 = 1.46 | A11V, Q14K, E28Q, K30Q, G86D, S95N, V99A, I133L, L225I, I251M, K305R |
M7: β | 138 | -5547.37 | p= 0.015, q= 0.074 | Not allowed |
M8: β &ω | 140 | -5527.82 | p 0 = 0.96; p= 0.09, q= 0.38; p 1 = 0.039, ω= 2.20 | A11V, Q14K, K30Q, S95N, V99A, I133L, L225I |
Branch-site models | Â | Â | Â | Â |
Taxaceae-Cephalotaxaceae | Â | Â | Â | Â |
Model A: ω 2 = 1, fixed | 139 | -5533.19 | p 0 =0.857, ω 0 =0.053;p 1 =0.061,ω 1 =1;p 2a +p 2b = 0.082, ω 2 = 1 | Not allowed |
Model A: ω 2 estimated | 140 | -5530.95 | p 0 =0.891, ω 0 =0.06;p 1 =0.078,ω 1 =1;p 2a +p 2b = 0.03, ω 2 = 2.55 | A11V, V99A, I133L |
Taxus | Â | Â | Â | Â |
Model A: ω 2 = 1, fixed | 139 | -5535.98 | p 0 =0.852, ω 0 =0.057;p 1 =0.106,ω 1 =1;p 2a +p 2b = 0.042, ω 2 = 1 | Not allowed |
Model A: ω 2 estimated | 140 | -5533.12 | p 0 =0.86, ω 0 =0.06;p 1 =0.103,ω 1 =1;p 2a +p 2b = 0.027, ω 2 = 5.9 | K30Q |
Torreya | Â | Â | Â | Â |
Model A: ω 2 = 1, fixed | 139 | -5538.23 | p 0 =0.82, ω 0 =0.059;p 1 =0.106,ω 1 =1;p 2a +p 2b = 0.073, ω 2 = 1 | Not allowed |
Model A: ω 2 estimated | 140 | -5538.33 | p 0 =0.82, ω 0 =0.059;p 1 =0.106,ω 1 =1;p 2a +p 2b = 0.071, ω 2 = 1.02 | None |
Podocarpaceae | Â | Â | Â | Â |
Model A: ω 2 = 1, fixed | 139 | -5527.9 | p 0 =0.84, ω 0 =0.049;p 1 =0.057,ω 1 =1;p 2a +p 2b = 0.099, ω 2 = 1 | Not allowed |
Model A: ω 2 estimated | 140 | -5523.16 | p 0 =0.89, ω 0 =0.065;p 1 =0.063,ω 1 =1;p 2a +p 2b = 0.047, ω 2 = 2.41 | A11V, G86D, V99A, I133L |
Podocarpus I | Â | Â | Â | Â |
Model A: ω 2 = 1, fixed | 139 | -5537.56 | p 0 =0.786, ω 0 =0.05;p 1 =0.084,ω 1 =1;p 2a +p 2b = 0.129, ω 2 = 1 | Not allowed |
Model A: ω 2 estimated | 140 | -5533.91 | p 0 =0.727, ω 0 =0.058;p 1 =0.091,ω 1 =1;p 2a +p 2b = 0.181, ω 2 = 1.12 | None |
Podocarpus II | Â | Â | Â | Â |
Model A: ω 2 = 1, fixed | 139 | -5530.31 | p 0 =0.81, ω 0 =0.054;p 1 =0.093,ω 1 =1;p 2a +p 2b = 0.097, ω 2 = 1 | Not allowed |
Model A: ω 2 estimated | 140 | -5526.95 | p 0 =0.85, ω 0 =0.056;p 1 =0.096,ω 1 =1;p 2a +p 2b = 0.056, ω 2 = 3.31 | S143A, T262V |
Model | np | â„“ | Parameters | Positively selected sites |
Cephalotaxaceae | Â | Â | Â | Â |
Model A: ω 2 = 1, fixed | 139 | -5537.3 | p 0 =0.82, ω 0 =0.058;p 1 =0.102,ω 1 =1;p 2a +p 2b = 0.077, ω 2 = 1 | Not allowed |
Model A: ω 2 estimated | 140 | -5536.84 | p 0 =0.862, ω 0 =0.059;p 1 =0.105,ω 1 =1;p 2a +p 2b = 0.032, ω 2 = 2.68 | None |