Question: Looking for Population Genetics Simulation Software
2
gravatar for xescape
2.8 years ago by
xescape20
xescape20 wrote:

Hi,

I'm looking for software that can be used generate simulated genomes using a Forward-Time approach starting from a number of ancestors. The end result should either be a number of complete genomes, or a table containing SNPs at maybe 500k positions from all members of the resulting population. The population should be haplodiploid with mating, where recombination (crossover/conversion) occurs.

The biggest difficulty is that I need every recombination event during mating to be recorded in some readable fashion, as I'm using this to test another software I made that identifies these events.

I've tried simuPOP, SLiM, and GPopSim, but they either do not work with nucleotides or are not able to record the events. Does anyone know of a tool that's able to do this?

To be specific, I'm looking for something like:

parentA, parentB, offspringC, crossover @ chrI 2000

parent A, parentB, offspringC, conversion @ chrII 4000 - 5000

in the output in some fashion.

Thanks for any help or information.

population simulation genome • 1.0k views
ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 2.8 years ago by xescape20
1

I have no clue about population genetics but I heard a tool called SIMCOAL which might be useful for you.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by geek_y9.8k
1

Have a look at this and this lists.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by h.mon26k

any updates after 2.2 years?

ADD REPLYlink written 7 months ago by Shicheng Guo7.6k
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