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Differential expression analysis was calculated using the software edgeR [ 67].
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Solubility and supersaturation were calculated using the software package EQ3/6.
Centiles were calculated using the software LMS ChartMaker.
All statistical analysis was calculated using SAS 9.2 (SAS Institute, Cary, NC) software.
Robustness analysis: Robustness of the model output was calculated using the simulation software SBML-SAT [ 22].
CI was calculated using the CIA software.
AMOVA analysis based on haplogroup frequencies was calculated using the Arlequin 3.5 software.
The tail length was calculated using the image analysis software (TriTek CometScoreTM).
The significance of enrichment was calculated using the Gene Set Enrichment Analysis (GSEA) software [ 12].
Statistical analysis was carried out using SPSS 13.0 software, and the survival rate was calculated using the Kaplan-Meier method.
The diversity indices including AMOVA (analysis of molecular variance) based Fst analysis were calculated using ARLEQUIN 3.01 software [35].
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