How Can I Simulate A Shrinking Population With A Selective Sweep?

Question

[user]

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?

Answer 1

[Leonor Palmeira]

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.

Answer 2

[Adam]

SFS_CODE should be able to do this I think.