Codon substitution model | LRT | Models | Parameters |
---|---|---|---|
Branch | H0: Same ω for all branches H1: Different ω for all branches | Model 0: one-ratio model vs Model 1: free-ratios model. | Model 0: model = 0, fix_omega = 0, omega = 0 Model 1: model = 1, fix_omega = 0, omega = 0 |
Branch | H0: Same ω for all branches H1: A different ω for the foreground branch | Model 0: one-ratio model vs Model 2: different ratio in the specified branch | Model 0: model = 0, fix_omega = 0, omega = 0 Model 2: model = 2, fix_omega = 0, omega = 0 |
Branch | H0: ω = 1 for the foreground branch H1: ω ≠ 1 for the foreground branch | Model 2: different ratio in specified branch vs Model 2 fix ω: ratio = 1 in the specified branch | Model 2: model = 2, fix_omega = 0, omega = 0 Model 2 fix ω: model = 2, fix_omega = 1, omega = 1 |
Branch-Site | H0: Same ω for all sites among branches. H1: Different ω for all sites in the foreground branch. | A: different ratio per site in specified branch vs A1: ω ratio = 1 per site in the specified branch | A: model = 2, NSsites = 2, fix_omega = 0 A1: model = 2, NSsites = 2, fix_omega = 1, omega = 1 |