Hi there,
I have used 454 GFLX to (de-novo) sequence two plant ecotypes (two divergent populations which adapted to each of their own habitats) by polling 16 individuals from each ecotype. To date, i have finished assembling, SNPs and Indel detection. And i also calculate population parameters like Watterson's Theta (θ = 4Neμ), Pi (which is expected to be equal to theta under neutral equilibrium). However, i am not sure whether it is possible to inferring some other parameters like Ne (effective population size), divergence time of the two ecotypes.
By the way, i would like to know how do you identify SNP outliers for you data if you have done or doing the same thing. Is it good to use a Fst based approach or Fisher exact test?
Elzed
What system did you use to detect SNPs and INDELs in your dataset?
Sorry fot the late reply. By system, do you mean softwares? I tried Mosaik && BWA-SW + Samtools to do alignment and SNP calling.