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| dbalick [2023/01/09 15:38] – ivan | dbalick [2023/01/09 15:38] – ivan |
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| //**This is work in progress, so please use with caution!!**. I will be updating this (with any bug fixes) as needed. | //**This is work in progress, so please use with caution!!**. I will be updating this (with any bug fixes) as needed.// |
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| **neqPopDynx** (__N__on-__eq__uilibrium __Pop__ulation __Dyn__ami__x__) is a flexible, terminal-based Wright-Fisher simulator scripted in Python 3 for outputting temporal data. Allele frequencies evolve independently in the infinite recombination limit to assess properties of the allele frequency //probability distribution// and are subject to user-specified rates of mutation and back mutation rates (allowing for recurrence), selection and dominance coefficients, initial population size, and a choice of pre-specified demographic changes in the population size with specifiable parameters (e.g., growth rate of exponential expansion, bottleneck start time, duration, and diploid size). The purpose of this simulator is to produce robust temporal output of the non-central moments, central moments, and/or cumulants of the allele frequency probability distribution averaged over L independent sites starting from the same initial frequency p_0=n/2N. This allows for comparison to analytic results of the equilibration process towards mutation-selection-drift balance and the dynamics of fully non-equilibrium demographic scenarios (e.g., exponential growth, population bottlenecks). | **neqPopDynx** (__N__on-__eq__uilibrium __Pop__ulation __Dyn__ami__x__) is a flexible, terminal-based Wright-Fisher simulator scripted in Python 3 for outputting temporal data. Allele frequencies evolve independently in the infinite recombination limit to assess properties of the allele frequency //probability distribution// and are subject to user-specified rates of mutation and back mutation rates (allowing for recurrence), selection and dominance coefficients, initial population size, and a choice of pre-specified demographic changes in the population size with specifiable parameters (e.g., growth rate of exponential expansion, bottleneck start time, duration, and diploid size). The purpose of this simulator is to produce robust temporal output of the non-central moments, central moments, and/or cumulants of the allele frequency probability distribution averaged over L independent sites starting from the same initial frequency p_0=n/2N. This allows for comparison to analytic results of the equilibration process towards mutation-selection-drift balance and the dynamics of fully non-equilibrium demographic scenarios (e.g., exponential growth, population bottlenecks). |
| Written by Daniel J. Balick | Written by Daniel J. Balick |
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| //For citations, please reference our [[https://doi.org/10.1016/j.ajhg.2021.12.001|American Journal of Human Genetics]] manuscript. | //For citations, please reference our [[https://doi.org/10.1016/j.ajhg.2021.12.001|American Journal of Human Genetics]] manuscript.// |
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| **simDoSe** (__Sim__ulate __Do__minance and __Se__lection) is a fast Wright-Fisher simulator for arbitrary diploid selection evolving through realistic human demography. | **simDoSe** (__Sim__ulate __Do__minance and __Se__lection) is a fast Wright-Fisher simulator for arbitrary diploid selection evolving through realistic human demography. |