title: Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.
abstract: 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/.
authors: Laboratoire de Génétique Cellulaire, INRA, 24 Chemin de Borde Rouge, Auzeville CS 52627, Castanet Tolosan Cedex, 31326, France. simon.boitard@toulouse.inra.fr
authors: Simon
authors: S
authors: Boitard
authors: Robert
authors: R
authors: Kofler
authors: Pierre
authors: P
authors: Françoise
authors: David
authors: D
authors: Robelin
authors: Christian
authors: C
authors: Schlötterer
authors: Andreas
authors: A
authors: Futschik
mesh_terms: D000818:Animals; D005787:Gene Frequency; D023281:Genomics / Q000295:instrumentation*; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011784:Quail / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000295:instrumentation*; D012984:Software