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We then conducted maximum likelihood-based sequence analysis using RAxML (8.0.0 [ Stamatakis et al. 2008], GTRCAT model, 1,000 bootstrap inferences) on the CIPRES Science Gateway (Miller et al. 2010) (https://www.phylo.org/portal2/login!input.action last accessed January 13 , 2015.
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RAxML was run on the above optimal 20 partitions, each partition with a GTR + I + Γ model and all model parameters estimated, executing 1000 rapid bootstrap inferences before a thorough ML search.
Statistical support was evaluated with 1,000 nonparametric bootstrap inferences.
For each of these models we conducted 200 inferences on the original alignment to search for the best ML tree and 1,000 bootstrap replicates enabling the bootstopping option for the frequencies based criterion [ 68].
Where he particularly excels is in his inferences on the profound cultural consequences of these philosophies.
Permutation and bootstrapping methods are used to perform inference on the change points.
These could always indicate noise resulting from systematic errors in inference, but the high bootstrap values on the DdDp trees suggests otherwise.
Maximum Likelihood phylogenetic inference on the concatenated set was done using RAxML [ 79], using the GAMAWAG model and 1000 bootstrap replicates.
Bootstrap values on the consensus trees were derived from 1000 bootstrap replicates.
Moreover, if we switch to the bootstrap, precision depends on the number of bootstrap samples.
The inference engine performs inference operation on the fuzzy rules.
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