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The data were imputed using the 'ice' command of Stata, using 45 imputation models set at 20 cycles.
Here, Otsu's thresholding using "graythresh" command of MATLAB software was performed for converting gray scale image into its binary one [ 20].
The designed primers were then used for in silico PCR experiments using the ipcress command of the exonerate package [ 58] with the default options.
We used the same overdispersion parameter for each model, calculated from the autosomal inbreeding model using the "c_hat" command of the "AICcmodavg" package.
Unbound structures were aligned with the corresponding complex using the "align" command of PyMOL [28].
Mutants were generated by side chain replacement using the MUTATE command of the WHATIF package [33],[33].
Construction and diagonalization of the covariance matrix was performed using the g_covar command of GROMACS.
Projection of structures onto eigenvectors was performed using the g_anaeig command of GROMACS.
Next, the coverage and nucleotide differences were extracted using the pileup command of the Maq program.
Arithmetic and harmonic means were calculated using the sump command of MrBayes.
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