Question: Simulation Negative Selection
1
gravatar for Rubal7
7.5 years ago by
Rubal7770
Rubal7770 wrote:

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

genome selection • 1.9k views
ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 7.5 years ago by Rubal7770
2
gravatar for tiagoantao
7.5 years ago by
tiagoantao660
United States of America
tiagoantao660 wrote:

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.

ADD COMMENTlink written 7.5 years ago by tiagoantao660

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

ADD REPLYlink written 7.5 years ago by Rubal7770
1
gravatar for Adam
7.5 years ago by
Adam990
United States
Adam990 wrote:

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

ADD COMMENTlink written 7.5 years ago by Adam990

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

ADD REPLYlink written 7.5 years ago by Rubal7770
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