Sentence examples for datasets were calculated with from inspiring English sources
Phylogenies and 100 bootstrap supports for all datasets were calculated with PhyML v3.0 [ 80] with the LG [ 81] amino acid substitution model, estimated portions of invariable sites, estimated Γ distribution parameter, four rate categories, estimated amino acid frequencies, and an NJ starting tree.
The ratio scores are then summarized in box plots and the difference between all the ratios of both datasets is calculated with a non-parametric, two-sided Wilcoxon rank-sum test implemented in R. Figure 2 illustrates this evaluation step.
The presence of the TCAGATCTG motif (with a stringency of 1 mismatch) or of the two MIR168b-specific sub-motifs identified by the point of a 14 bp insertion in Aethionema grandiflora (stringency of 2 mismatches; Additional File 2B) in the miRNA and the TAIR7 3' and 5' UTR datasets was calculated with the EMBOSS fuzznuc application.
The log-likelihood of each dataset is calculated with the benchmark set.
For correlation analysis, all datasets were calculated for correlation efficiency and were considered significant at p<0.05.
The validation metrics were calculated with two different datasets; a dataset of event documentations reporting flooded areas and a dataset of insurance claims.
False-discovery rates (FDR) were calculated with 1000 permutations of the dataset using the High-Throughput GoMiner software, bolding highlights those terms with a FDR <5%.
Genetic distances (absolute number of changes and uncorrected "p" distances) were calculated with Paup ver. 4.0b2a [32] based on the combined dataset (Dataset S4).
BI trees were calculated with mrbayes 3.1[ 77] for protein and nucleotide datasets by running two analyses each consisting of two simultaneous runs with four heated chains per run.
