Exact(26)
The likelihood difference between 2 trees inferred using 2 different models M1 and M2 might fluctuate due to various error factors, e.g., numerical problems and local optimizations.
The predictive power of each individual variable in the model was tested using ratio likelihood tests which computed a chi-square statistic based on the log likelihood difference between the full model and a reduced model that excluded that variable.
c Likelihood difference between the collapsed tree and the actual best tree.
The likelihood difference between independent and dependent (= correlated) models was estimated for 1000 simulations.
Twice the log likelihood difference between the two compared models (2Δl), was compared against χ 2 with 1 df.
The likelihood difference between winged and unwinged morphs of males is not significant (proportional likelihoods of 0.84 and 0.15, respectively).
Similar(34)
b Range of the likelihood differences between collapsed tree and best tree obtained over 100 simulations, representing the null distribution for the main likelihood comparison.
In this way we obtained a null distribution of 100 likelihood differences between best and collapsed tree (the null hypothesis tree).
In the Log-likelihood Ratio Test (LRT) the significance of the likelihood differences between the model with free estimate of Ka/Ks and the null model is estimated by the quantity 2ln(L1/ L0), which approximates a χ2 distribution.
In all four loci tested, several basal branches could be simultaneously collapsed without significant likelihood differences between the collapsed and the best gene tree as compared to the null distribution obtained with simulations: four branches for RAG1, five for vWF, six for BRCA1, and five for 12S16S (Table 4).
A likelihood ratio test for positive selection was performed with a χ2-distribution on two degrees of freedom by comparing twice the log-likelihood difference between a nearly-neutral model (M1a, in which ω cannot exceed 1) and a selection model (M2a) that included an additional category for ω>1 [57].
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