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We ran maximum likelihood analyses using the program GARLI [64] until 10,000 generations revealed no significant improvement of likelihood scores of the topology.
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Performance improvements of likelihood-based methods over Rg become more significant when identification is performed on the dataset with higher percentage of missing data and larger noise.
The likelihood of independent allele frequency model showed that the improvement of the likelihood of clustering dropped dramatically for K above 5.
EM guarantees the improvement of the likelihood at each iteration, converging to a local optimum [30].
We used the GTR+I+G model as selected by MrModeltest for the combined dataset and ran analyses until 10,000 generations revealed no significant improvement of the likelihood scores of the topology.
This is coherent with the very weak improvement of the likelihood between M1a and M7/M8 models for these two groups.
Table 1 shows that improvement of logarithm likelihood of the alignment is significant when α AB or α ML is used.
Multivariate analyses were carried out to identify patient, disease or treatment factors associated with likelihood of overall improvement and likelihood of response in at least one organ.
Further, the improvement of the Log Likelihood beyond the optimal model is expected to be negligible.
A significant improvement of the model likelihood under unconstrained conditions, when compared to the constrained model, would be taken as evidence for a difference in variance components among periods.
The best model for each fleece trait was chosen after testing for improvement of the log-likelihood values.
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