Looking for Population Genetics Simulation Software

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7.5 years ago

xescape ▴ 20

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.

genome simulation population • 1.9k views

ADD COMMENT • link updated 6.9 years ago by Biostar 20 • written 7.5 years ago by xescape ▴ 20

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

ADD REPLY • link 7.5 years ago by GouthamAtla 12k

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Have a look at this and this lists.

ADD REPLY • link 6.9 years ago by h.mon 35k

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any updates after 2.2 years?

ADD REPLY • link 5.4 years ago by Shicheng Guo ★ 9.4k

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