PIFs. PIFs (acronym of Pool_Ind_Freq_SNP.xls) is an excel encoded application (compatible with OpenOffice Calc) that includes various graphical and numerical outputs which allow NGS practitioners to assessing and comparing the precision in allele frequency estimation for both pool and diploid individual SNP data under various sampling, coverage and experimental error designs. Details about the underlying assumptions and mathematical derivations are provided in Gautier et al. (2013).
Poolne_estim. Poolne_estim is a program implementing a Markov Chain Monte Carlo algorithm to sample the posterior distribution of the different parameters underlying the Bayesian hierarchical model described in Gautier et al. (2013). It is primarily aimed at estimating in Pool-Seq experiment the effective diploid size of pools/replicates (e.g. identified by molecular barcodes) from SNP allele count data. Note that each pool (or replicate) are assumed to originate from the same population.
Gautier M, Foucaud J, Gharbi K, Cezard T, Galan M, Loiseau A, Thomson M, Pudlo P, Kerdelhue C & Estoup A, 2013. Estimation of population allele frequencies from next-generation sequencing data: pooled versus individual genotyping. Molecular Ecology, 22(4): 3766-3779. (https://doi.org/10.1111/mec.12360)
