This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Sfscode- Specifying Inital Allele Frequencies

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

simulation genome
• 2,311 views • link
updated by rh7967 • rh7967 • written by Rubal7 Rubal7

1 answer

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

• 0 views • link
written by rh7967 • rh7967

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

• 0 views • link
written by Rubal7 Rubal7

Log in to answer this question.

More posts like this