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The maximum likelihood score equations in matrix notations can be written as X^{T} left( {varvec{y} -varvec{mu}} right) = 0,where, (varvec{mu}= left( {mu_{1}, ldots,mu_{n} } right)^{T}).
However, the maximum likelihood score often overfits the data because it does not reflect the model complexity.
Such weights could be an average of bootstrap scores of the tree's internal branches, a maximum parsimony or maximum likelihood score or a Bayesian posterior probability estimate.
For each offspring tested, candidate parents were assigned with at least 95% confidence using exclusion probability first and the maximum likelihood score second (Marshall et al. 1998).
Using MODELTEST [ 31], the model of sequence evolution with the highest maximum likelihood score as shown by the Akaike Information Criterion method was obtained and then implemented in maximum likelihood analyses in PAUP (v. 3.1, [ 32]).
A fundamental observation in this study is that searching for supertrees that optimize the maximum likelihood score under the S2+CAT model improved tree accuracy, a trend that we found quite surprising.
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Based on maximum likelihood scores, the identity of a face in the video sequence was recognized.
The marker order along LGs was determined based on maximum likelihood scores.
Trees sampled before the cold chain reached stationarity based on plots of the maximum likelihood scores were discarded.
The homogeneous models of nucleotide substitution (GTR and TVM) and the maximum likelihood scores for the best trees (ranging from 10147.76 to 2496.26) are shown in Table 1.
Our algorithm takes advantage of the weights (e.g., least-square scores, posterior probabilities, maximum likelihood scores or p-values) assigned to the gene trees as well as the weights associated with the tree clusters (e.g., cluster's bootstrap score or posterior probability) to infer the species dominant and alternative evolutionary histories.
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