Snpsim assumes a population of a fixed size from which individuals are chosen to reproduce and move from generation to generation. The process continues until a fixed amount of time has elapsed and then a new population is created to replace the old population. SNPsim is a windowed program. The window size is determined at initialization and is changeable at run-time. It is important to realize that SNPsim does not determine the window size on its own. It assumes that the window size is a fixed parameter and that it is explicitly set. It is not recommended to change the window size after initialization. This can have dramatic consequences for accuracy and runtime. Instead, when SNPsim is executed for the first time, set the window size as desired and leave it alone. If the window size is chosen too large, SNPsim will run slower than if the window size is chosen too small. If it is chosen too small, it is difficult to make sure that the intended window size is actually set. Since there is not much to do, the window size can be changed at run-time, if necessary.
Window Size Description:
SNPsim’s window size determines the size of the current population, the number of generations in which this population may be alive and the number of random generations that will occur in between window updates. The window size is determined at initialization and is changeable at run-time. It is important to realize that SNPsim does not determine the window size on its own. It assumes that the window size is a fixed parameter and that it is explicitly set. It is not recommended to change the window size after initialization. This can have dramatic consequences for accuracy and runtime. Instead, when SNPsim is executed for the first time, set the window size as desired and leave it alone. If the window size is chosen too large, SNPsim will run slower than if the window size is chosen too small. If it is chosen too small, it is difficult to make sure that the intended window size is actually set. Since there is not much to do, the window size can be changed at run-time, if necessary. When SNPsim is closed, the window size is discarded. Since 4f8c9c8613 promfit
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