Genepop protocols

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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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Maintainer


  • person_outline François Rousset <>

Additional information


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

Publications for Genepop

Genepop in pipelines

 (112)
2018
PMCID: 5817159
PMID: 29468047
DOI: 10.1002/ece3.3821

[…] established in this study will aid in combating the dearth of genetic data available for labeobarbus and other cyprinids., raw sequence data, processed input files for the final dataset (structure, genepop, fineradstructure, arlequin, genetix, diyabc, geste/bayescan, and vcf), and regular expressions for removing adapter pollution are available from the dryad digital repository: […]

2018
PMCID: 5819644
PMID: 29463303
DOI: 10.1186/s13104-018-3249-1

[…] microsatellite markers were then tested for the presence of null alleles with the software microchecker []. linkage disequilibrium and hardy–weinberg equilibrium were tested with the software genepop []. in order to control for multiple testing, the p value threshold was adjusted with bonferroni correction. number of alleles na, observed heterozygosity ho and expected heterozygosity […]

2018
PMCID: 5859023
PMID: 29555926
DOI: 10.1038/s41598-018-23004-2

[…] were estimated using arlequin v. 3.11. deviations from hardy-weinberg equilibrium (hwe) were characterized by the inbreeding coefficient (fis) with genetix v. 4.05 and p-values where calculated genepop v. 4.2. putative scoring errors were checked with micro-checker v. 2.2.3 and freena v. 9.3 was used to to evaluate possible differences between estimates of global and pairwise fst values […]

2018
PMCID: 5870918
PMID: 29587859
DOI: 10.1186/s13104-018-3301-1

[…] stuttering, large allele dropout, and/or the presence of null alleles. alleles were analyzed for deviations from hardy–weinberg expectations within sites and overall linkage disequilibrium using genepop on the web [, ]. significance tests with multiple comparisons used an adjusted critical value based on the b-y false discovery rate (fdr) []. structure ver. 2.4.3 [] was used to determine […]

2017
PMCID: 5301200
PMID: 28186200
DOI: 10.1038/srep42416

[…] significance of temporal trends was tested using the mann-kendall trend test implemented in past. pairwise differences in allelic frequencies between decades were estimated for each river using genepop. fst values of genetic differentiation were estimated using genetix v.4.04 and significances were determined with 1000 permutations to correct for simultaneous tests, strict bonferroni […]


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Genepop in publications

 (1494)
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 […]

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 […]

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 […]

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, […]

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 […]


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

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