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The quality of the genotypic dataset was assessed using M ICRO-C HECKER[ 38].
Rate heterogeneity within the dataset was assessed using the likelihood-ratio test (LRT) [ 74, 75].
Initially, the variable dataset was assessed using the Shapiro-Wilk test.
The performance of NEWHYBRIDS to detect purebred and hybrid individuals with the present microsatellite dataset was assessed using simulated data generated by HYBRIDLAB [ 25].
For each validated strain (Table 1), sequence similarity to all sequences in E2 protein dataset was assessed using BLAST [ 27] search.
The temporal signal of the dataset was assessed using Path-O-Gen, which showed an r-squared value of 0.53 with the best-fitting root (date range 29 years) [ 23].
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Peak intensity data generated using this dataset were assessed using histograms and dot plots to determine a cut-off and the results for each sample scored as high or low (above or below the cut-off).
The biological functionality of genes in the two datasets was assessed using Gene Ontology [ 32] classifications.
Statistical significance for gene expression and probe methylation from cell line and TCGA datasets were assessed using the Mann-Whitney test with Bonferroni correction across groups.
The detection accuracy of the data matrices W and S in distinguishing the four interaction categories (SL, SS, PE and PS) from the background variability (i.e. the complement of the category in the dataset under evaluation) was assessed using the receiver operating characteristic (ROC) curves [61].
Since no external validation dataset is currently available, model performance was assessed using the internal dataset in two approaches.
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