Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
dbalick [2015/06/05 01:11]
dbalick [Code]
dbalick [2015/06/05 02:09]
dbalick
Line 1: Line 1:
-========  ​Daniel Balick's software and resources page ========+ 
 + 
 + 
 + 
 +{{:​evolution_laptop.jpg?​nolink&​670|}} 
 + 
 + 
 + 
 + 
 +========  ​DANIEL BALICK'S SOFTWARE AND RESOURCES ​======== 
 + 
 + 
 +---- 
 + 
 + 
  
 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]]). 
  
-====  README ==== 
  
-{{README_burden_sim.pdf|README}} 
  
 +=====  MUTATIONAL BURDEN SIMULATOR =====
 +
 +
 +----
 +
 +
 +written by David Reich
 +
 +
 +
 +==== Simulating selection and dominance in a non-equilibrium demography ====
 +
 + 
 +How does a population bottleneck impact the mutation burden under differing dominance and selection coefficients?​
 +
 +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 ====
  
-====  Code ====+  * {{README_burden_sim.pdf|README}}
  
-{{burden_sim_code.zip}} 
  
 +====  CODE (written in C) ====
  
-====  Compiled code ====+  * {{burden_sim_code.zip}}
  
-Burden simulation for simple (square) bottleneck: ​ {{burden_sim_SimpleBN}} 
  
-Burden simulation for Gravel demography: ​ {{burden_sim_Gravel}}+====  COMPILED CODE ====
  
-Burden simulation for Tennessen demography: ​ {{burden_sim_Tennessen}}+  * 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}}