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The background-subtracted data were then filtered based on confidence using the Benjamini Hochberg false-discovery rate and on the fold change using the cut-off point of a 2-fold difference implemented Table in the GeneSpring software package.
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Tukey's significant differences implemented in SYSTAT were used to compare selection coefficients among the five inoculants.
The relative area difference measure, implemented in the evaluation of the works [2, 26], measures the extent of the automatically segmented region that does not coincide with the expected correct region.
To more objectively quantify this difference, we implemented SHIRPA protocol designed for comprehensive phenotype assessment [15].
To quantitatively compare trees among simulations, we used the symmetric tree distance [ 64, 65] (symmetric difference test implemented in PAUP* 4.0b10).
Potential HGT candidate genes were identified across 18 Pseudomonas genomes using %codon bias and %G + C difference analysis, implemented in SIGI-HMM program [ 52].
A closed testing of prespecified primary and secondary endpoints based on the treatment difference was implemented in order to preserve the overall type I error rate at 5%.
The geographical structure of the populations was further analysed using Monmonier's maximum difference algorithm, implemented in BARRIER 2.2 software (Manni et al. 2004).
The Tukey Honest Significant Difference method implemented in the function TukeyHSD of the R statistical package was used to compute confidence intervals of pairwise means among the different data sets to test which means of the Ks distributions differ significantly.
The electrostatic potential around the 3D structures was computed by numerically solving the Poisson Boltzmann equation using the finite difference method implemented in the DelPhi program within Discovery Studio 2.1 (Accelrys, San Diego, CA).
The results of this analysis are now included in the revised article, as follows: To investigate the possibility that the perceived advantages of the WNC-based selection over standard techniques is explained by the relatively larger gene sets detected by the former method, an independent GO enrichment analysis that accounts for this difference was implemented.
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