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dbalick [2023/01/09 15:36] – ivan | dbalick [2023/01/09 15:48] (current) – ivan | ||
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- | //**This is work in progress, so please use with caution!!**. | + | //**This is work in progress, so please use with caution!!**. |
**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 // | **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 // | ||
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Files for neqPopDynx_v1.5: | Files for neqPopDynx_v1.5: | ||
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=====simDoSe===== | =====simDoSe===== | ||
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- | Written by Daniel J. Balick | + | Written by Daniel J. Balick |
- | //For citations, please reference our [[https:// | + | |
- | // | + | //For citations, please reference our [[https:// |
**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. | ||
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====Features==== | ====Features==== | ||
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* Entirely command line-based, so the only needed software is Python 2.7 and the numpy, scipy, and pandas packages. | * Entirely command line-based, so the only needed software is Python 2.7 and the numpy, scipy, and pandas packages. | ||
* Flexible output specification, | * Flexible output specification, | ||
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====Additional details, instructions for running, examples==== | ====Additional details, instructions for running, examples==== | ||
Please see the simDoSe [[https:// | Please see the simDoSe [[https:// | ||
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====Downloading simDoSe==== | ====Downloading simDoSe==== | ||
simDoSe is available for [[https:// | simDoSe is available for [[https:// | ||
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=====srMLgenes===== | =====srMLgenes===== | ||
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**srMLgenes** is a web-based visualization tool to analyze the enrichment of pre-specified or user-uploaded gene sets for strong recessive purifying selection (or for strong additive selection, neutrality, and other diploid selection coefficients of interest). | **srMLgenes** is a web-based visualization tool to analyze the enrichment of pre-specified or user-uploaded gene sets for strong recessive purifying selection (or for strong additive selection, neutrality, and other diploid selection coefficients of interest). | ||
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====Features==== | ====Features==== | ||
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The web-based version of srMLgenes is available [[http:// | The web-based version of srMLgenes is available [[http:// | ||
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===== Mutational Burden Simulator ===== | ===== Mutational Burden Simulator ===== | ||
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+ | Written by David Reich | ||
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+ | //For citations, please reference our [[http:// | ||
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- | Written by David Reich\\ | ||
- | //For citations, please reference our [[http:// | ||
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==== Simulating selection and dominance in a non-equilibrium demography ==== | ==== Simulating selection and dominance in a non-equilibrium demography ==== | ||
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How does a population bottleneck impact the mutation burden under differing dominance and selection coefficients? | How does a population bottleneck impact the mutation burden under differing dominance and selection coefficients? | ||
Below is the code for **burden_sim**, | Below is the code for **burden_sim**, | ||
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====Files for burden_sim==== | ====Files for burden_sim==== | ||
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* Burden simulation for Gravel demography: | * Burden simulation for Gravel demography: | ||
* Burden simulation for Tennessen demography: | * Burden simulation for Tennessen demography: | ||
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//This page is managed by DJB and does not necessarily reflect the Sunyaev lab as a whole.// | //This page is managed by DJB and does not necessarily reflect the Sunyaev lab as a whole.// | ||