|Title||Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples|
|Publication Type||Journal Article|
|Year of Publication||2013|
|Authors||Boitard, S, Kofler, R, Francoise, P, Robelin, D, Schlötterer, C, Futschik, A|
|Journal||Molecular Ecology Resources|
|Keywords||allele frequency spectrum, hidden Markov models, next generation sequencing, pooled DNA, selective sweeps.|
Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/.