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Genodive specifications

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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 citations

 (151)
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

[…] 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 […]

library_books

Meta populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

2018
Front Zool
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 […]

library_books

Is the Success of Plant Invasions the Result of Rapid Adaptive Evolution in Seed Traits? Evidence from a Latitudinal Rainfall Gradient

2018
Front Plant Sci
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 […]

library_books

Genetic and morphological support for possible sympatric origin of fish from subterranean habitats

2018
Sci Rep
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 […]

library_books

Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North East Atlantic using a random forest classification approach

2018
Sci Rep
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 […]

library_books

Genetic evidence for panmixia in a colony breeding crater lake cichlid fish

2018
Sci Rep
PMCID: 5773479
PMID: 29348515
DOI: 10.1038/s41598-018-19266-5

[…] sensitive to homozygosity were also conducted using a reduced number of loci (see results). data are available in table ., summary statistics of diversity and population structure were calculated in genodive v2.0b27 and statistical significance assessed with 9999 permutations. infinite allele model was assumed for calculating the analysis of molecular variance (amova). fis statistics […]


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

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