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As duplicate simulations exhibited equivalent characteristics (Table S1 and Figure S3), single trajectories for each structure were randomly selected for a more detailed description.
Duplicate simulations of 100 ns each were performed in each case.
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In the 1956 classic horror film Invasion of the Body Snatchers, the citizens of the fictional town of Santa Mira, California are replaced by perfect physical duplicates, simulations grown from plantlike pods.
We duplicated the simulations using a simple temperature-index model best fitted to the data and results were poorer, R2<0.8.
We duplicated the simulation scenarios described in Table 2 in [ 21]: 50 population replicates with biallelic markers initially at equal frequencies with spacings of 0.25, 0.5, and 1.0 cM, an effective population size and a sample size of N = N s = 100, and a time t = 100 since the initial mutation.
"Of course, we cannot reproduce each and every situation that may occur in the actual battlefield, but the major items can be duplicated in these simulations," said Gen. Yuji Fujinawa, chairman of the joint staff council for Japan's Defense Agency.
In each simulation, duplicate status was randomly assigned to the sequenced genes for each strain.
The reason: One case containing the PEC of this true signal had been identified as a duplicate after the first simulation, and was excluded in the second simulation.
Figure 2 shows that the prediction of the model describes the known number of duplicates in a simulation that are observed to segregate at a given age and fail to fix.
Simulation of duplicate gene retention showed that patterns of retention varied significantly depending upon model parameters (fig. 3).
While most of our results therefore concern stochastic simulations, we duplicated many of our experiments using quasi-deterministic models and used the presented technique of frequency domain analysis to investigate the differences.
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