Genodive protocols

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Genodive specifications

Information


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
Stability No
Maintained No

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Publication for Genodive

Genodive in pipelines

 (15)
2017
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 [] and principle component analysis (pca) using the adegenet v2.0.1 package for statistical software r v3.2.4 (https://www.r-project.org/). in addition, the population differentiation […]

2017
PMCID: 5383466
PMID: 28405300
DOI: 10.1002/ece3.2819

[…] using the option “–write_single_snp.”, to assess differentiation among colonies and levels of genetic diversity, we calculated global and population diversity and f‐statistics for each snp using genodive (meirmans & van tienderen, ) and stacks, respectively. major allele frequencies, percentage of polymorphic sites, and π indicate the general level of genetic diversity in a population. f […]

2017
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, ). in addition, we tested each locus‐pair within populations for evidence of linkage‐disequilibrium (ld) using genepop (raymond & rousset, ; […]

2017
PMCID: 5498645
PMID: 28680075
DOI: 10.1038/s41598-017-04849-5

[…] and 1000 bootstrapping replicates for k values 1, 2, 3, 4 and 5 (fig. ). to further understand the distribution of genetic variation across geography, we calculated principal components in genodive 2.0 and principal coordinates in genalex 6.5, . pca analysis of both snps and microsatellites are shown in the main text (fig. ) and principal coordinates in the supplement (fig. )., to test […]

2017
PMCID: 5552028
PMID: 28796789
DOI: 10.1371/journal.pntd.0005718

[…] within them. data are transformed using a pca and then clusters are identified using discriminant analysis. we assessed genetic differentiation among population pairs by calculating fst values with genodive v. 2.0b27 []. we also ran isolation by distance (ibd) analyses for all populations and for all ca populations using genodive v. 2.0b27., while the snp chip has 50,000 probes, only 27,674 […]


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Genodive in publications

 (147)
PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y

[…] 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 calculated by both popoolation and popoolation2. as allele […]

PMCID: 5910556
PMID: 29721030
DOI: 10.1186/s12983-018-0266-9

[…] biosystems). the alleles are provided in additional file : table s7., observed and expected heterozygosities for microsatellites were calculated using msa version 4.05 [] and for mhc alleles using genodive []. average relatedness was determined with the program coancestry []. to investigate the structure between and within the farms we used the software structure [] for the microsatellite […]

PMCID: 5835042
PMID: 29535741
DOI: 10.3389/fpls.2018.00208

[…] whether the studied populations are formed by few successful clonal lineages or by several multi-locus lineages, we estimated the extent of clonal reproduction in our aflp dataset using the software genodive 2.0b17 (). we choose genodive because it has been extensively employed to estimate clonal diversity on marine organisms (e.g., ) and plants (e.g., ; ) using aflp markers. briefly, genodive […]

PMCID: 5811452
PMID: 29440653
DOI: 10.1038/s41598-018-20666-w

[…] in addition, two supplementary k-means clustering analyses, the bayesian information criterion (bic; schwarz) and the calinski–harabasz pseudo-f-statistic, were performed on individuals using the genodive v.2.0b25 program. for these k-mean clustering analyses, a simulated annealing method was used, where the optimal k value was determined via checking k values ranging from 1 to 5 for 5,000 […]

PMCID: 5775277
PMID: 29352185
DOI: 10.1038/s41598-018-19323-z

[…] assignment probabilities were calculated in adegenet. analyses of molecular variance (amova), weir and cockerham estimators of fst, and summary statistics (ho, he, gis, π) were calculated in genodive. p-values for fst were fdr adjusted for multiple comparisons using a benjamini-hochberg correction in the r-package p-adjust. isolation-by-distance was assessed using a mantel test […]


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

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