Skip to main content

Table 3 Likelihood estimates of Proteinase K (S08.054) gene family for site models in PAML

From: Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Model

np

Parameter estimates (Proportion p, omega ω)

lnL

LRT pairs

Df

2ΔlnL

P

Positively selected sites (BEB)

site model

M0:one ratio

116

ω = 0.12397

−19267.73

M0/M3

4

1537

0.00

 

Model M3:Discrete

120

P 0  = 0.23156

−18499.23

     

p 1 = 0.41651

p 2 = 0.35193

ω0 = 0.01542

ω1 = 0.08491

ω2 = 0.31104

M1a(neutral)

117

p 0  = 0.66046

−18857.30

M1a/M2a

2

0

1

 

p 1 = 0.33954

ω0 = 0.12388

ω1 = 1.00000

Model 2a: Positive Selection

119

p 0  = 0.66046

−18857.30

     

p 1 = 0.09285

p 2 = 0.24669

ω0 = 0.12388

ω1 = 1.00000

ω2 = 1.00000

Model 7: beta

117

p =0.81898

−18473.64

M7/M8

2

0

1

 

q =4.31422

Model 8 :

119

p 0  = 0.99999

−18473.64

     

p = 0.81899

q =4.31430

p 1 = 0.00001

ω = 1.00000

  1. Selection analysis by site models. np: number of free parameters. lnL: log likelihood. LRT: likelihood ratio test. df: degrees of freedom. 2∆lnL: twice the log-likelihood difference of the models compared. Bold: P < 0.05