The Bayesian-based maximum likelihood test implemented in Geneclass2 v2.0 [ 46] has been shown to be effective in genotype assignment, even when populations deviate from Hardy-Weinberg equilibrium [ 65, 66].
We surveyed this dataset for signatures of sequence evolution, selection and/or adaptation using the McDonald-Kreitman test [ 26] and codon-based maximum likelihood analyses [ 27, 28].
To test the selective pressure acting on OR genes in primates, we performed codon-based maximum likelihood method using CODEML nested in PAML package (Yang 2007).
Based on the maximum likelihood test, the hypothesis of the equality of frontier function in all of the subsectors, except the basic metal industry (BMI) subsector, was rejected, and this indicates that these functions can separately be estimated.
The OT is the maximum likelihood test based on orthogonal decomposition of genotype scores.
The window identified as least likely due to chance, is subsequently evaluated by a maximum likelihood test with a test decision based on a Monte-Carlo simulated P-value [ 5].
Differences between survival rates were tested, using the Maximum Likelihood test of Wald, sandwich version.
Nevertheless, MDL1 was subjected to the maximum likelihood tests for positive selection with PAML and HyPhy.
The significance of variables was tested using maximum likelihood tests.
Attempts at a heuristic to automatically determine motif width in a deterministic (Expectation-Maximization, or EM-based) algorithm have included functions based on the maximum likelihood ratio test (LRT) [ 11], methods based on V -fold cross-validation [ 7] and the Bayesian Information Criterion (BIC) [ 12].
Tests for positive selection were based on maximum likelihood analysis of dN/dS values among C. elegans paralogs, essentially as described previously [ 6].
