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Simulation Negative Selection

Hello,

Does anyone know a genetics simulation software that can simulate regions under long-term negative-selection? Coalescent simulators such as msms are only capable of simulating selection at specific sites. We are interested in simulating negative selection over an entire region (so multiple sites simultaneously). I have a suspicion that some forward simulators are capable of doing this but I have no experience with forward simulators. If anyone thinks they know a simulator that can do what we are looking for please let me know. Thanks in advance!

Best,

Rubal

selection genome
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updated by Biostar Biostar • written by Rubal7 Rubal7

2 answers

Simupop can do this. It is robust, well documented and with many examples. But it is a programmable simulator: you have to know (or learn) Python. I cannot think of a non-programmable simulator that can do this (easypop comes to mind, but will not do it). Another possibility might be Rmetasim (in R), but I really do not know if it does what you want. simupop is a very safe bet if you know python or are willing to learn.

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written by tiagoantao tiagoantao

Thanks this looks promising, I'll look into it, appreciate your help!

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written by Rubal7 Rubal7

SFSCODE can simulate data under a huge range of models: http://sfscode.sourceforge.net/SFS_CODE/index/index.html

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written by Adam Adam

Ah yes I've heard of SFSCODE, this sounds good thanks

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written by Rubal7 Rubal7

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