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Although neighbor-joining methods are less accurate than the other methods such as most likelihood methods, SDSE is clustered with the GAS strains as their closest relative.
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The glmM phylogenetic trees based on the neighbor-joining (data not shown) and maximum likelihood methods grouped most of the sequences from the Hong Kong strains in the same branch.
Most applications of GLMMs use approximate likelihood methods to estimate model parameters.
Maximum likelihood methods seek to identify the most likely tree, given the available data.
The estimations were done using maximum likelihood methods, which is considered one of the most appropriate approaches for small samples with autocorrelated errors [21],[21].
The three maximum likelihood methods were intermediate, with the quantitative method most similar to exclusion allowing zero mismatches, and the perturbed method with an assumed error most similar to exclusion allowing three mismatches.
Likelihood methods are commonly used to estimate the most likely network that is, the set of causal relationships among the different variables that better agrees with the data.
We compared FastTree's speed and accuracy to those of PhyML 3.0 and RAxML 7, the most popular maximum-likelihood methods.
Maximum likelihood methods are explored to obtain reliable estimates.
Sibship analysis and parentage reconstruction of the WWP gemplasm were conducted using the most accurate full-pedigree likelihood method of the COLONY program [ 59].
Several approaches for parameter estimation were proposed in the literature but the maximum likelihood method is the most commonly employed.
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