Hi all, I am often wondering if some groups have already started developing forward population simulators based on GPUs to simulate >1 Mb chunks of DNA, > 10,000 individuals. Thanks in advance!!!!
Hi Andre, thanks for your reply! It's really great if you could develop a simulator that accomodates so many individuals. The features I am looking for are the following:
- a simulator using the Wright-Fisher model.
- accommodating heterogeneous recombination rates across simulated segment. I would like to be able to specify the probability function of recombination events across the simulated segments (like sfs_code does for example).
- enabling introduction by the user of mutations at user-specified coordinate, generation time and with a user-specified selection coefficient.
If your simulator does all this that would be great. Otherwise I will be happy to give you feedback as an intensive forward in time population simulator user.
I wish you the best with the development of your simulator.
David.
Hi Andre,
I am interested in both fitness-affecting mutations occurring at random and by the ability of introducing some where and when I want.
For example some population geneticist may be interested in estimating the power of his new statistical method to detect sweeps. To do so he may use say a 100kb segment, and may look at the ability to detect sweeps 100 generations after the fixation of an advantageous mutation. This kind of analysis is greatly simplified if you can introduce yourself an advantageous mutation in the middle of the 100kb segment at the right time given average time to fixation.
In brief there are many caes where it is useful to control where and when some mutations occur, especially when testing selective hypotheses.
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