Sfscode- Specifying Inital Allele Frequencies

Question

[Rubal7]

Hello all,

Does anybody know if it is possible to specify starting allele frequencies and/or specific nucleotide sequences for simulations in SFSCODE? We are trying to simulate regions with low vs high amounts of sequence diversity.

Thanks in advance,

Alex

[Aaronquinlan]

0

I don't know the answer, but I would advise that you email the author, Ryan Hernandez. http://profiles.ucsf.edu/ProfileDetails.aspx?Person=5323269

Answer 1

[rh7967]

Hi Alex,

Sadly, initial allele frequencies are not something that you can specify directly. In terms of frequencies, you can only specify terminal frequencies. The reason is that sfs_code needs to burn-in the population to mutation/selection balance. If you want to give me more specifics about what you are trying to do, there are potentially some work arounds, otherwise simuPOP may do some forward simulations conditional on a trajectory (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0030047), or you could use something like selsim (http://www.well.ox.ac.uk/~spencer/SelSim/) to simulate under the structured coalescent.

Best,

Ryan

[Rubal7]

Thanks very much for getting in touch. We will think about what you have said and then maybe get in touch with more specifics.