Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

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...

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Vydané v:	Molecular ecology resources Ročník 13; číslo 2; s. 337 - 340
Hlavní autori:	Boitard, Simon, Kofler, Robert, Françoise, Pierre, Robelin, David, Schlötterer, Christian, Futschik, Andreas
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Oxford Blackwell Publishing Ltd 01.03.2013 Blackwell Wiley Subscription Services, Inc Wiley/Blackwell
Predmet:	allele frequency spectrum Amphibia. Reptilia Animal and plant ecology Animal, plant and microbial ecology Animals Biological and medical sciences Computer programs computer software cost effectiveness design detection estimation Fundamental and applied biological sciences. Psychology Gene Frequency General aspects Genetics Genetics of eukaryotes. Biological and molecular evolution genomics Genomics - instrumentation hidden Markov models High-Throughput Nucleotide Sequencing information Internet Life Sciences Models, Genetic next generation sequencing Polymorphism, Single Nucleotide pooled DNA population Population genetics Population genetics, reproduction patterns Quail - genetics Resource sampling selective sweeps Sequence Analysis, DNA - instrumentation Software Synecology Vertebrates: general zoology, morphology, phylogeny, systematics, cytogenetics, geographical distribution allele frequency spectrum Program next generation sequencing pooled DNA Markov model Ophidia Spectrum hidden Markov models Vertebrata Gene frequency DNA Reptilia selective sweeps Sequencing hidden markov model pooled dna selective sweep newt generation sequencing
ISSN:	1755-098X, 1755-0998, 1755-0998
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Popis
Shrnutí:	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/.
Bibliografia:	Austrian Science Fund - No. P19467 ArticleID:MEN12063 PHC PHC Amadeus - No. 25154QH istex:BADD969FFCCB87409A860D29D3F395FFBF32B712 ark:/67375/WNG-MK81LBS8-Z ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 PMCID: PMC3592992
ISSN:	1755-098X 1755-0998 1755-0998
DOI:	10.1111/1755-0998.12063