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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Bibliographic Details
Published in:Molecular ecology resources Vol. 13; no. 2; pp. 337 - 340
Main Authors: Boitard, Simon, Kofler, Robert, Françoise, Pierre, Robelin, David, Schlötterer, Christian, Futschik, Andreas
Format: Journal Article
Language:English
Published: Oxford Blackwell Publishing Ltd 01.03.2013
Blackwell
Wiley Subscription Services, Inc
Wiley/Blackwell
Subjects:
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
Online Access:Get full text
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Summary: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/.
Bibliography: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
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PMCID: PMC3592992
ISSN:1755-098X
1755-0998
1755-0998
DOI:10.1111/1755-0998.12063