Table 5 Parameter estimates and likelihood ratio tests for the branch-site models

M1: Neutral (k=2)

1

-47271.650

p ₀ =0.774, (p ₁ =0.226)

Model A (I-1)

3

-47231.883

p ₀ = 0.416, p ₁ = 0.123, (p _2a +p _2b =0.461), ω₂ =1.291

Model A vs M1: 79.535

2

0.000

Site for foreground lineage: 15 (at p>0.95)

Model A (II-1)

3

-47271.650

p ₀ =0.774, p ₁ = 0.226, (p _2a +p _2b =0.000), ω₂=2.639

Model A vs M1: 0.000

2

1.000

Model A (II-2)

3

-47271.650

p ₀ = 0.774, p ₁ = 0.226, (p _2a +p _2b =0.000), ω₂ =1.000

Model A vs M1: 0.000

2

1.000

Model A (II-3)

3

-47253.663

p ₀ =0.740, p ₁ = 0.214, (p _2a +p _2b =0.046), ω₂=28.900

Model A vs M1: 35.974

2

0.000

Site for foreground lineage: 1 (at p>0.95)

Model A (II-4)

3

-47264.889

p₀=0.707, p₁= 0.207, (p _2a +p _2b =0.085), ω₂=1.506

Model A vs M1: 13.523

2

0.001

Model A (II-5)

3

-47257.978

p ₀ =0.718,p ₁ = 0.210, (p _2a +p _2b =0.072), ω₂=3.022

Model A vs M1: 27.345

2

0.000