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EGN is a script implemented in Perl.
All calculations were performed using a script implemented in the R software, version 2.7.1 http://www.r-project.org.org
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We conducted single marker and haplotype TDT association analysis using a custom script implemented in R statistical software and based on Transmit [14], and the equivalent FBAT approach [15] for comparison of the results.
The feature selection was completed using a custom script implemented in SAS.
We used a custom Python script implemented in the goatools package (https://github.com/tanghaibao/goatools) to extract all GO terms and the corresponding descriptions from the sub-ontology "biological process" and to map this information to the ortholog clusters.
According to the SIA script implemented in the optimized manifold shown in Fig. 1a, nitrate reduction occurred as buffered sample was propelled through the micro-column for 25 s by a peristaltic pump revolving at 50% speed.
For the F-test, the FatiGO script implemented in R was used.
We used the MMRR function script implemented in R 3.0.2 (Wang 2013).
The residuals from the fit of the model to the data were visualized using the R script implemented in Treemix.
A total of 43,197 sequenced contigs of 'Chinese Antique' were screened for SSR motifs with the Msatfinder script implemented in PERL (http://www.genomics.ceh.ac.uk/msatfinder).ac.uk/msatfinder
Using the resulting pan-genome matrix we determined the genetic loci uniquely associated with the ST131 group versus the non-ST131 group using the compare_BSR python script implemented in the LS-BSR package.
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