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Among widely used methods are likelihood ratio tests of codon substitution models, which detect selection on the protein sequence using the comparison of nonsynonymous (amino-acid altering) and synonymous (amino-acid preserving) substitution rates (for review see [ 37]).
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Such methods are likelihood-based mixed effects model (LME) [ 9, 10] and generalized estimating equations (GEE) methods.
COLONY [ 8] and COLONY 2.0 [ 9] are likelihood methods which construct half-sibling families.
Our study demonstrates that the explicit methods are in all likelihood also influenced by experience-based knowledge.
These methods are pseudo-maximum likelihood and moment estimation.
Maximum likelihood methods are explored to obtain reliable estimates.
All methods are in a penalized likelihood framework with weighted L1 regularization.
The classical SDE parameter estimation methods are largely based on likelihood estimation, which is computationally expensive.
In Section 2 Maximum Penalized Likelihood Methods are introduced.
As a result, the likelihood methods are not suitable for populations with large N e.
Least Squares (LS) and Maximum Likelihood (ML) methods are employed to estimate parameters of the models.
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