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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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Versioning


No version available

Maintainer


  • person_outline François Rousset

Additional information


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

Publications for Genepop

Genepop citations

 (2000)
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

[…] maximum coverage to 500 to call SNPs at this stage. As Popoolation2 is not capable of calculating diversity indices such as Tajima’s π and Watterson’s θW, total heterozygosity was calculated from the GenePop file used to detect outliers (see section below) using Genodive [].To assess the effects of population-specific resampling on intraspecific variation, we compared the frequencies of SNPs calcu […]

call_split

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
call_split See protocol

[…] using 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 Informa […]

library_books

Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae), a major vector of stolbur phytoplasma: Evidence of cryptic speciation

2018
PLoS One
PMCID: 5940214
PMID: 29738577
DOI: 10.1371/journal.pone.0196969

[…] on, as well as overall and per host-plant association. Deviations from Hardy-Weinberg (HW) were estimated using Micro-checker []. Linkage disequilibrium (LD) was checked with the web-based version of Genepop [] using the settings 1,000 batches and 10,000 de-memorizations and iterations per batch. The sex-linked locus C147 was omitted in both analyses. Significance levels for multiple comparisons w […]

call_split

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
call_split See protocol

[…] st 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 replicates w […]

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, th […]

call_split

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
call_split See protocol

[…] alleles (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 c […]

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

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