[sfscode-users] selective sweep in time series data

[Florian C. <flo...@gm...>]

Hi,

I would like to simulate a selective sweep in a time series experiment,
i.e. with a sample of the allele frequencies before and after the sweep.
First I simulated the desired selective sweep pattern without considering
time series data using following command:

./sfs_code 1 1 -t 0.01 -r 0.05 -n 25 -L 1 10000 -a N --mutation 0 S 5000 G
1000 --trackTrajectory S 5000 R 1 1 A G 0 -TE 3

Then I tried to create time series data by copying the ancestral population
at time 0 and immediately stopping the simulation for this copy (keeping
the rest of the command as it was for the sweep):

./sfs_code 2 1 -TS 0 0 1 -TE 0 0 -t 0.01 -r 0.05 -n 25 -L 1 10000 -a N
--mutation 0 P 1 S 5000 G 1000 --trackTrajectory S 5000 R 1 1 A G 0 -TE 3

The problem is that these simulations ran for days (compared to minutes in
the case without time series data) and did not produce the expected sweep
pattern.

If anyone has an idea on this, I'd be grateful to get some advice.

Best wishes,
Florian