Genepop pipeline

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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Documentation


Maintainer


  • person_outline François Rousset <>

Additional information


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

Publications for Genepop

Genepop IN pipelines

 (23)
2017
PMCID: 5415527
PMID: 28479988
DOI: 10.1002/ece3.2831

[…] to calculate 95% confidence intervals. in addition, the significance of population divergence was also assessed through tests of allele frequency homogeneity among populations. this was performed in genepop (raymond & rousset, 1995; rousset, 2008) using the g test, which computes the p‐value for the observed differences in frequencies between populations for all loci, using a markov chain […]

2017
PMCID: 5433974
PMID: 28515868
DOI: 10.1002/ece3.2860

[…] equilibrium (hwa) using genodive v.2.0b27 (meirmans & van tienderen, 2004). in addition, we tested each locus‐pair within populations for evidence of linkage‐disequilibrium (ld) using genepop (raymond & rousset, 1995; rousset, 2008), and we estimated the frequency of null alleles present for each locus and population using freena (chapuis & estoup, 2007). the degree […]

2017
PMCID: 5433974
PMID: 28515868
DOI: 10.1002/ece3.2860

[…] whether genetic differentiation was correlated with geographic distances, the presence of isolation‐by‐distance was estimated by performing linear‐regression of f st / (1‐f st), calculated in genepop, versus the linear distance between populations (km) in r v. 3.1.3 (r core team 2015). finally, to examine historical relationships among populations a “neighbornet” network was reconstructed […]

2017
PMCID: 5485074
PMID: 28214367
DOI: 10.1111/mec.14066

[…] appropriate unbiased estimator of divergence (balloux & lugon‐moulin 2002). potential association between f st and geographical distance was explored by a mantel test of matrix correlation using genepop 4.0.10 (rousset 2008). an additional measure of differentiation (jost's d est) was calculated in genalex 6.501 (peakall & smouse 2012) using all samples. population substructuring […]

2017
PMCID: 5756880
PMID: 29321915
DOI: 10.1002/ece3.3667

[…] (meirmans & van tienderen, 2004). departures from hardy–weinberg equilibrium (hwe) and the presence of locus‐by‐locus linkage disequilibrium (ld) were then estimated with the software package genepop (raymond & rousset, 1995; rousset, 2008). estimates of population differentiation based on f st were generated using freena (chapuis & estoup, 2007) to account for the potential […]

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

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