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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