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

Branchsite models
    
TaxaceaeCephalotaxaceae
    
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
    
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
    
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
    
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
    
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
    
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

ℓ

Parameters

Positively selected sites

Cephalotaxaceae
    
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
