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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 citations

 (8)
library_books

Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates

2017
Nat Commun
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 […]

library_books

Nucleotide diversity inflation as a genome wide response to experimental lifespan extension in Drosophila melanogaster

2017
BMC Genomics
PMCID: 5237518
PMID: 28088192
DOI: 10.1186/s12864-017-3485-0

[…] 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”, while “--the […]

call_split

Genome wide analysis of long term evolutionary domestication in Drosophila melanogaster

2016
Sci Rep
PMCID: 5177908
PMID: 28004838
DOI: 10.1038/srep39281
call_split See protocol

[…] or 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 to o […]

library_books

Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population

2016
Genome Biol Evol
PMCID: 4898808
PMID: 27189991
DOI: 10.1093/gbe/evw094

[…] We used different methods to estimate the SFS of our NLR data. Pool-HMM () calculates an allele frequency spectrum (SFS) directly from the mapped reads and uses this as a prior to estimate SNP frequency at a given location. We used GATK to infer allele frequency […]

library_books

Whole Genome Sequencing Reveals Genetic Variation in the Asian House Rat

2016
PMCID: 4938650
PMID: 27172215
DOI: 10.1534/g3.116.029504

[…] 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, and […]

library_books

Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system

2016
BMC Genomics
PMCID: 4791783
PMID: 26979755
DOI: 10.1186/s12864-016-2556-y

[…] Sweeps were identified by Pool-hmm [], a hidden Markov model for detecting selective sweep based on Pool-Seq data. The parameters used in Pool-hmm were set to be “-n 100 -c 5 -C 400 -q 20 -e sanger -p -k 0.0000000001”, and “-- […]


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

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