Genodive pipeline

Genodive specifications


Unique identifier OMICS_20130
Name Genodive
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input files of both programs consist of tab-delimited text-files in specific formats.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Maintained No


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Publication for Genodive

Genodive IN pipelines

PMCID: 5242430
PMID: 28099434
DOI: 10.1371/journal.pntd.0005223

[…] vni populations (e.g. clinical and environmental, and according to the continent of origin) was calculated using the hierarchical analysis of molecular variance (amova) implemented in the software genodive v2.0 [51] and principle component analysis (pca) using the adegenet v2.0.1 package for statistical software r v3.2.4 ( in addition, the population differentiation […]

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

[…] of alleles (eff_n a), the average observed heterozygosity across loci (h o), the average inbreeding coefficient (g is), and the presence of deviation from hardy–weinberg 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, […]

PMCID: 5498645
PMID: 28680075
DOI: 10.1038/s41598-017-04849-5

[…] idation, and 1000 bootstrapping replicates for k values 1, 2, 3, 4 and 5 (fig. s4). to further understand the distribution of genetic variation across geography, we calculated principal components in genodive 2.055 and principal coordinates in genalex 6.562, 63. pca analysis of both snps and microsatellites are shown in the main text (fig. 2) and principal coordinates in the supplement (fig. s5)., […]

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

[…] (eff_num), the observed heterozygosity (h o), within‐population heterozygosity (h s), total heterozygosity (h t), and the inbreeding coefficient (g is) were all estimated using the software program genodive v.2.0b27 (meirmans & van tienderen, 2004). departures from hardy–weinberg equilibrium (hwe) and the presence of locus‐by‐locus linkage disequilibrium (ld) were then estimated […]

PMCID: 4761760
PMID: 26941944
DOI: 10.1002/ece3.1909

[…] for all downstream analyses the snps with more than two alleles were removed. finally, using plink 1.9 (purcell et al. 2007) all snps with more than 5% missing data were removed., genodive 2.0 (meirmans and van tienderen 2004) was used to calculate summary statistics, including the observed frequency of heterozygotes within sampling sites (ho), the expected frequency […]

Genodive institution(s)
Institute for Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam, Amsterdam, Netherlands

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