|Analyzing pooled sequenced data with selection|| Main project page|
Simulating evolution and then pooled sequencing
To do this we can use Dick Hudson's MS to lay down neutral variants (but the distribution really does not matter).
To do this we can use Kessner's Forqs. Forqs allows the user to specify the recombination rate file which might be useful in the future. Also Forqs was written in way with selection experiments in mind, they have functions such as "Quantitative Trait" that allows the user to define the fitness function in a complex way.
(1) draw a coverage (n) from Pois(λ) where
(2) fi (frequency of the ith SNP) ~