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Protocols

Genepop specifications

Information


Unique identifier OMICS_17393
Name Genepop
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License CeCILL version 2.1, GNU General Public License version 3.0
Computer skills Advanced
Version 4.6
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline François Rousset

Additional information


http://genepop.curtin.edu.au/

Publications for Genepop

Genepop citations

 (1537)
library_books

Complex signatures of genomic variation of two non model marine species in a homogeneous environment

2018
BMC Genomics
PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y

[…] of snps, and brandsebaai had the greatest (table ). as popoolation2 is not capable of calculating diversity indices (i.e. tajima’s π and watterson’s θw), we calculated total heterozygosity from the genepop files used in the outlier detection analyses. the total heterozygosity was highly similar between limpet populations, ranging between 0.082 to 0.084 (table ). the number of private snps (snps […]

library_books

Genetic characterization of indigenous goat breeds in Romania and Hungary with a special focus on genetic resistance to mastitis and gastrointestinal parasitism based on 40 SNPs

2018
PLoS One
PMCID: 5942826
PMID: 29742137
DOI: 10.1371/journal.pone.0197051

[…] snp viewer software (version 1.99, hoddesdon, uk). the raw allele calls received from lgc genomics were analyzed with klustercaller software from lgc genomics. linkage analysis was performed by genepop []. popgene 1.32 [] was used to calculate the deviation from hardy-weinberg equilibrium (hwe), observed (ho) and expected (he) heterozygosity values for each studied breed, polymorphic […]

library_books

Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds

2018
PLoS One
PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276

[…] for departure from hardy-weinberg equilibrium (hwe) was done using the markov chain monte carlo method (20 batches, 5,000 iterations per batch and a dememorisation number of 10,000) implemented in genepop version 4.0 software []. level of significance were adjusted using false discovery rate (fdr) procedure []., the fis for each population was calculated via bootstrapping using 1,000 […]

library_books

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction Associated DNA Sequencing

2018
Genes
PMCID: 5924560
PMID: 29673217
DOI: 10.3390/genes9040218

[…] and fixation index (f), were assessed at each locus and population levels using genealex version 6.5 []. the hardy-weinberg equilibrium (hwe) at each locus for each population was determined using genepop version 4.2 [,]. the polymorphism information content (pic) values were calculated using the program pic_calc version 0.6 []. to estimate the genetic variation among and within populations, […]

library_books

Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa

2018
PLoS One
PMCID: 5901919
PMID: 29659603
DOI: 10.1371/journal.pone.0194726

[…] (apriv) was estimated using gda v.1.0 []. fstat v.1.2 [] was used to calculate allelic richness (ar), thus correcting for different sample sizes, and inbreeding coefficient (fis). the package genepop v.1.2 [] was used to perform exact tests of hardy–weinberg equilibrium (hwe), and f-statistics estimated by weir and cockerhan []. population genetic structure was evaluated using a bayesian […]

library_books

Development of novel EST SSR markers for ploidy identification based on de novo transcriptome assembly for Misgurnus anguillicaudatus

2018
PLoS One
PMCID: 5896994
PMID: 29649332
DOI: 10.1371/journal.pone.0195829

[…] cervus 3.0 []. the polymorphism information content (pic) was calculated using the excel microsatellite toolkit v3.1 [], and deviation of hardy-weinberg equilibrium (phw) was evaluated with the genepop v 4.2 []., among the 98 primer pairs, 45 putative est-ssr markers exhibited polymorphism in diploids (). they were further tested in tetraploids. the na, he and shannon's diversity index […]


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Genepop institution(s)
Institut des Sciences de l’Evolution (UM2-CNRS), Université Montpellier 2, Montpellier, France

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