Pool‐hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples. (11th January 2013)

• Record Type: Journal Article
• Authors: Boitard, Simon; Kofler, Robert; Françoise, Pierre; Robelin, David; Schlötterer, Christian; Futschik, Andreas
• Is Part Of: Molecular ecology resources. Volume 13:Number 2(2013:Mar.)
• Page Start: 337
• Page End: 340
• Publication Date: 2013-01-11
• Subjects: Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12063
• Languages: English
• ISSNs: 1755-098X

Abstract

<abstract abstract-type="main" xml:lang="en" id="men12063-abs-0001"> <title>Abstract</title> <p>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/.</p> </abstract>