Our choice of sampling parameters, with 500 individuals sampled every 16 generations, represents an achievable experimental protocol (Barrick et al., 2010).
The value of n is fixed for a particular farm or, equivalently, sample parameter set, but due to the wide range of values quoted in the literature was treated as one of the sampled parameters, with values between 5 and 12 lactations.
For robustness calculations, concentration values of kinases and phosphatases were sampled in the range of 0.1-10 0.1-10times reference values (reference values are theiralues used foreferenceulations in the unperturbed system) and the sample parameter sets with their sampling ranges are givalues Additional file 2: Table S3.
The sample parameters and trees were summarized with removal of the first 10%% as burn-in and tracer was used to check for convergence for each analysis.
The supervised dendrogram model generated (Fig. 9) with 39 samples (13 parameters with 3 replicates each) was validated through a permutation test that calculates the goodness of fit and the predictive ability of the model, represented by R2 and Q2, respectively.
Outputs were subsequently obtained by running the model for all sampled parameter vectors with the outputs renormalized according to the assigned weights.
The default BADGER sampler parameters propose sorting inversions with high probability, neutral inversions (which do not change the reversal distance) with lower probability, and "bad" inversions (which increase the reversal distance) with still lower probability.
For the sampled parameters, expert opinion together with a range of published estimates has enabled the calculation of an appropriate range and distribution for their values, as described in Additional file 2: Table S2.
As previously noted, the posterior correlation between v and s can be high; hence, it might be advantageous to jointly sample these two parameters with a bivariate random walk MH sampler, as demonstrated with a different application by Ntzoufras [ 13].
Bayesian phylogenetic reconstruction was performed as for the Akirins, except with different sampling parameters for each gene family.
