How Can I Simulate A Shrinking Population With A Selective Sweep?
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11.9 years ago
user ▴ 20

I need to simulate a genomic region with a shrinking effective population size from 100 (past) to 30 (present). The region must include a selective sweep undergoing positive selection. any idea?

genetics simulation • 2.0k views
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Entering edit mode
11.9 years ago

I don't know of any tool that simulates this, so I guess you will have to implement a Monte Carlo simulation algorithm which includes the features that are believed to result from what you describe:

  • shrinking Ne -> incrinsing genetic drift -> higher rate of random fixation
  • strong positive selection -> higher dN/dS (>1)

Maybe you can use a sequence simulation software for the sequence evolution part (I developed alfacinha if you want to try it out), but you will definitely have to write a part of the implementation yourself.

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Entering edit mode
11.9 years ago
Adam ★ 1.0k

SFS_CODE should be able to do this I think.

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