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- | ======== Daniel Balick's software and resources page ======== | + | |
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+ | {{:evolution_laptop.jpg?nolink&670|}} | ||
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+ | ======== DANIEL BALICK'S SOFTWARE AND RESOURCES ======== | ||
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+ | ---- | ||
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This page contains links to various software resources associated with our research. Feel free to email [[dbalick@research.bwh.harvard.edu]] if you have any questions, comments, or suggestions. | This page contains links to various software resources associated with our research. Feel free to email [[dbalick@research.bwh.harvard.edu]] if you have any questions, comments, or suggestions. | ||
- | ===== Selection, dominance, and demographic history ===== | ||
- | Below is the code for **burden_sim**, a simulation of the mutation burden for two populations after a split, as described in Balick, et. al. "Response to a population bottleneck can be used to infer recessive selection" (2013 preprint available here: [[http://biorxiv.org/content/early/2014/03/21/003491| biorxiv]],currently under review). This simulation was also used in Do, et. al. "No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans" ([[No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans|Nature Genetics 2015]]). | + | |
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+ | ===== MUTATIONAL BURDEN SIMULATOR ===== | ||
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+ | ---- | ||
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+ | written by David Reich | ||
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+ | ==== SIMULATION WITH SELECTION, DOMINANCE, AND NON-EQUILIBRIUM DEMOGRAPHY ==== | ||
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+ | How does a population bottleneck impact the mutation burden under differing dominance and selection coefficients? | ||
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+ | Below is the code for **burden_sim**, a simulation of the mutation burden for two populations after a split, as described in Balick, et al., //Response to a population bottleneck can be used to infer recessive selection// (2013 preprint available here: [[http://biorxiv.org/content/early/2014/03/21/003491| biorxiv]],currently under review). This simulation was also used in Do, et al., //No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans// ([[http://www.nature.com/ng/journal/v47/n2/abs/ng.3186.html|Nature Genetics 2015]]). | ||
==== README ==== | ==== README ==== | ||
- | {{README_burden_sim.pdf|README}} | + | * {{README_burden_sim.pdf|README}} |
==== CODE (written in C) ==== | ==== CODE (written in C) ==== | ||
- | {{burden_sim_code.zip}} | + | * {{burden_sim_code.zip}} |
==== COMPILED CODE ==== | ==== COMPILED CODE ==== | ||
- | Burden simulation for simple (square) bottleneck: {{burden_sim_SimpleBN.zip}} | + | * Burden simulation for simple (square) bottleneck: {{burden_sim_SimpleBN.zip}} |
- | + | * Burden simulation for Gravel demography: {{burden_sim_Gravel.zip}} | |
- | Burden simulation for Gravel demography: {{burden_sim_Gravel.zip}} | + | * Burden simulation for Tennessen demography: {{burden_sim_Tennessen.zip}} |
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- | Burden simulation for Tennessen demography: {{burden_sim_Tennessen.zip}} | + |