Signatures of co-evolutionary host-pathogen interactions in the genome of the entomopathogenic nematode Steinernema carpocapsae

Table 4 Likelihood Ratio Tests (LRTs) performed for each selected branch

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

NSsites = 0 for all the branch models. kappa was estimated for each gene and fixed with fix_kappa = 1 and kappa = estimated value. For all the models these parameters were the same: noisy = 3, verbose = 0,runmode = 0, seqtype = 1, CodonFreq = 2, clock = 0, aaDist = 0, icode = 0, fix_alpha = 1, alpha = 0, Malpha = 0, ncatG = 10, getSE = 0, RateAncestor = 0, Small_Diff = .5e-6, cleandata = 1, method = 1

ISSN: 2730-7182