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dbalick [2015/06/05 00:06]
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dbalick [2015/09/20 01:41] (current)
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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, etal. "Response to a population bottleneck can be used to infer recessive selection" ​(2013 preprint available here: [[http://biorxiv.org/content/early/​2014/​03/​21/003491biorxiv]],currently under review).   This simulation was also used in Do, etal. "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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 + 
 +==== 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?​ 
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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., //Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck// ​([[http://journals.plos.org/plosgenetics/article?​id=10.1371/journal.pgen.1005436|PLOS Genetics 2015]]).   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.pdf|README}}+  * {{README_burden_sim_v0.pdf|README}} 
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 + 
 +====  CODE (written in C) ==== 
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 +  * {{burden_sim_code.zip}} 
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 + 
 +====  COMPILED CODE ==== 
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 +  * Burden simulation for simple (square) bottleneck: ​ {{burden_sim_SimpleBN.zip}} 
 +  * Burden simulation for Gravel demography: ​ {{burden_sim_Gravel.zip}} 
 +  * Burden simulation for Tennessen demography: ​ {{burden_sim_Tennessen.zip}} 
  
  
-====  Code ==== 
  
-{{burden_sim.h}} 
  
  
-====  Compiled code ==== 
  
-Burden simulation for simple (square) bottleneck: ​ {{burden_sim_SimpleBN}} 
  
-Burden simulation for Gravel demography:  ​{{burden_sim_Gravel}}+---- 
 +Note:  ​This page is managed by DJB and does not necessarily reflect the Sunyaev lab as a whole. ​
  
-Burden simulation for Tennessen demography: ​ {{burden_sim_Tennessen}}