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To answer both questions, we used the support vector machines (SVMs) method with bootstrapping.
A support tree-clustering method with bootstrapping using expression data was performed to statistically validate the tool.
Phylogenetic trees were constructed in MEGA4 through the Neighbor-joining (NJ) method with bootstrapping test (1000 replicates).
This means that Method 3, which is the method with bootstrapping and genotype optimisation, gave the best results for all values of noise.
Gene selection was carried out by the support vector machines method with bootstrapping, which allowed us 1) ranking the genes that were most important for classification quality and appeared most frequently in the classifiers (bootstrap-based feature ranking, BBFR); 2) ranking the samples, and thus detecting cases that were most difficult to classify (bootstrap-based outlier detection).
A support tree clustering method with bootstrapping (ST) and a principal component analysis (PCA) using expression data were performed to statistically validate the tool.
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Paralogs were removed and the query sequence plus resultant hit sequences were used to infer the evolutionary history using the Neighbor-Joining [ 75] and Maximum Likelihood [ 76] methods with bootstrapping (1000 replicates) using MEGA5 [ 77].
Second, graphical modeling methods combined with bootstrapping methods show substantial age declines for both focal and non focal cues, dfocal = −0.50 and dnonfocal = −0.72, respectively.
Phylogenetic tree was constructed using neighbor-joining method with bootstrap (1000 replicates) by Kimura 2-parameter model using MEGA 5.1 program.
Phylogenetic trees were constructed using the MEGA 6.0 software program (Tamura et al. 2013), based on representative sequence for each OTU/aOTU, by neighbor-joining (NJ) method with bootstrap values calculated from 1000 replications.
ClustalW [93] multiple protein alignments were used to construct phylogenetic trees as determined by the Neighbor Joining method with bootstrap re-sampling (detailed in the legends for Figures 1), using MEGA3.1 [94].
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