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Perl scripts were used for data manipulation.
Stata version 11 (StataCorp LP, College Station, TX) was used for data manipulation and analysis.
Microsoft Office Excel 2007 will be used for data manipulation and SPSS version 16 for the main data analyses.
Matlab (Mathworks, Natick, MA, USA) and the PLS toolbox (Eigenvector Research, Wenatchee, WA, USA) were used for data manipulation and PCA.
The R Software v. 2.15.2 (R Core Team 2012) was used for data manipulation and graphical output using the ggplot2 (Wickham, 2009) and the doBy (Hojsgaard et al. 2012) packages.
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The comprehensive Ensembl Perl API is widely used for data access and manipulation by bioinformaticians and Perl is an ideal scripting language for bulk sequence manipulation.
SPSS package version 16.0 was used for data management and manipulation.
BEDtools and liftover utilities were used for data extraction, variant manipulation and overlap of genome annotations [ 107, 108].
Besides copyright protection, watermarking may be used for data monitoring, fingerprinting, and observing content manipulations.
We used IBM SPSS Statistics 20 for data manipulation and data management and SAS 9.3 for data analyses.
For data capture we used the 4D database software suitable for a simultaneous data entry by several people, for data manipulation we used Microsoft Office Access 2003.
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