Re: [sfscode-users] bacterial recombination

[Tatum M. <tmo...@wi...>]

Hi Ryan,

For the simulation with gene conversion:
sfs_code 1 5 -t 0.0014 -L 1 2516575 -H 0.00063 1549 -P 1 -n 13 -Td 0 4 -TE
0.03

For the simulation without gene conversion:
sfs_code 1 5 -t 0.0015 -L 1 4411532 -P 1 -n 200 -Td 0 25 -TE 0.051

I could use the exact same parameters with and without gene conversion if
that would be helpful. I had already done these simulations, so they were
easy to look at.

Tatum


On Mon, Sep 14, 2015 at 6:55 PM Ryan Hernandez <rh...@gm...> wrote:

> Hi Tatum,
>
> Can you remind me what parameters you are using for the two sets of
> simulations you mention here?
>
> Thanks,
>
> Ryan
>
> On Mon, Sep 14, 2015 at 3:20 PM, Tatum Mortimer <tmo...@wi...>
> wrote:
>
>> Hi Ryan,
>>
>> This reply is regarding a previous question about simulating bacterial
>> recombination. I wasn't a member of the mailing list then, and I can't
>> figure out how to respond to that message specifically. I've recently been
>> using SFS_CODE to simulate bacterial populations, including gene
>> conversion. When I run a recombination detection program (BRATNextGen) on
>> the results of the simulation, tracts of similar size to my input on the
>> command line are detected. I also double checked this by running a strictly
>> clonal simulation, and BRATNextGen detected no recombination. In your
>> previous answer, you said that gene conversion only works in diploids and
>> tetraploids. However, it appears that gene conversion is occurring in my
>> haploid simulations.
>>
>> Best,
>> Tatum
>>
>>
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>