For simulations using this shuffling procedure, we simulated 300 cells in each session on a linear track and randomly sampled 15 of these for further analysis.
For all the best-fit procedure, we simulated each alternative scenario 105 times and compared the simulated statistics to the observed statistics computed from our empirical dataset (20 re-sequenced regions).
To illustrate this procedure, we simulated the system for different channel codes in the same RCPC family, with rates equal to 1/3, 4/11, 2/5, and 4/9 [13], for Foreman QCIF at f D T s=0.005, R B=144 kbps, and C=150 ms. From Eq. (1), the corresponding source coding rates are 48, 52.4, 57.6, and 64 kbps, respectively.
Using this procedure we simulated populations of various sizes, which we used as the initial populations for the artificial selection simulations.
To determine the robustness of the above-described procedure, we simulated a draft assembly by using Sanger read samples of the complete genomes of different E. coli strains at low coverage (1x) (see Methods).
In order to exclude the possibility that the virus had been inactivated during infusion procedure, we simulated the conditions of the virus administration protocol by keeping the A7 74) virus -containing sterile saline infusion bag on ice for 3 h 25 min.
To double check our randomization procedure, we have simulated an ensemble of configuration model networks [44], whose in- and out-degree sequences are extracted from different realizations of our content-based model.
In addition, we have performed a parametric bootstrap procedure, in which we simulated alignments from the maximum-likelihood tree and re-calculated dates from the same maximum-likelihood topology with branch lengths optimized for each simulated alignment.
The procedure we used to simulate three-way admixed individuals is similar to what is used in HAPMIX (Price et al. 2009) for two-way admixtures.
