Pool-hmm specifications

Information


Unique identifier OMICS_05825
Name Pool-hmm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Pool-hmm

Pool-hmm in publications

 (7)
PMCID: 5691062
PMID: 29146998
DOI: 10.1038/s41467-017-01658-2

[…] the 6 nfs samples were classified as nfs1 (n1, n9, n12, and n16) and nfs2 (n3 and n6) according to the pca clusters. two methods were used to detect the possible sweep regions within population. (1) pool-hmm: sequencing reads within population were merged together and then mapped to the reference genome (dm3) using bwa with default parameters. the parameters in pool-hmm were set to be “-n 100 -c […]

PMCID: 5237518
PMID: 28088192
DOI: 10.1186/s12864-017-3485-0

[…] watterson's θ and tajima’s d with the window size set to 10 kb. heterozygosity was estimated using a 100 kb sliding window with a step of 10 kb., putative selective sweep regions were detected with pool-hmm [], a hidden markov model for finding selective sweep signatures from pool-seq data. the parameters used in pool-hmm were “-n 100 -c 5 -c 400 -q 20 -e sanger -p -k 0.0000000001”, […]

PMCID: 5177908
PMID: 28004838
DOI: 10.1038/srep39281

[…] footprints of selection across the genome, we relied on a hidden markov model developed with the intention to detect sweeps in pooled sequence data, developed by boitard et al., implemented in the pool-hmm software package. their method involves estimating the allele frequency spectrum (afs) across genomic regions and detecting distortions relative to the background afs, which are expected […]

PMCID: 4898808
PMID: 27189991
DOI: 10.1093/gbe/evw094

[…] genetics statistic π () was computed based on the estimated minor allele frequencies using snpgenie (). the folded site frequency spectrum (sfs) estimations were done using several methods. pool-hmm () was run to calculate the allele frequency in our data (option -spectrum) directly from the alignment file. these data were fed back into pool-hmm (option -estim) to estimate absolute […]

PMCID: 4938650
PMID: 27172215
DOI: 10.1534/g3.116.029504

[…] snps, the distance between neighboring neutral snps was set to at least 100,000 bp., to identify footprints of selection in the ahr genome, we estimated genome-wide allele frequencies using the pool_hmm program (, , ) with the following options: -c 20, –q 20, -k 1e-10, –pred, and –theta 0.0018. pool_hmm estimates allele frequencies at each polymorphic site based on a probabilistic model, […]


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Pool-hmm institution(s)
Laboratoire de Génétique Cellulaire, INRA, Auzeville CS, Castanet Tolosan, France

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