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Statistical inference was conducted using the negative binomial GLM fitting and Wald significance tests.
Bayesian inference was conducted with SAMCAT software (Sensitivity Analysis and Markov Chain simulations Applied to Transfer models) which launched the simulations through the embedded simulation engine GNU-MCSim, and automated their configuration and post-processing.
Phylogenetic tree inference was conducted in MEGA4 [15] using the Neighbor-Joining method [16] whereas the evolutionary distances were computed applying the Maximum Composite Likelihood method [17].
Statistical inference was conducted in two stages.
This inference was conducted using Rannala's Markov chain Monte Carlo (MCMC) framework (Rannala and Yang 2003).
Posterior inference was conducted after discarding the 'burn-in' iterations, based on 20,000 samples.
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The inference is conducted in a Bayesian framework that provides a better way to take into account the uncertainty in the model parameters when building the IDF curves.
On the other hand, a strong case has been made that processing related to inference is conducted within the SN alone [20], [21].
While this distinction gets blurred when inference is conducted with undirected graphical models, Bayesian networks provide an obvious incentive for taking it into account.
Phylogenetic analyses using a partitioned Bayesian inference were conducted in MrBayes 3.1.2 [ 35].
The inference is conducted on sampled haplotypes for which an IBD score is calculated using shared haplotype frequency.
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