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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 citations

 (189)
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

[…] ion2 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 frequenci […]

library_books

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species

2018
Microbiome
PMCID: 5932900
PMID: 29720271
DOI: 10.1186/s40168-018-0467-7

[…] We employed the AMOVA [] implemented in GenoDive v.2.0 to estimate overall and pairwise levels of genetic divergence as FST. We assumed an infinite alleles model [] and employed 999 permutations to estimate the probability of homogeneity. I […]

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

[…] 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 data. […]

call_split

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
call_split See protocol

[…] 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 us […]

call_split

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
call_split See protocol

[…] al. 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 per […]

call_split

From conservation genetics to conservation genomics: a genome wide assessment of blue whales (Balaenoptera musculus) in Australian feeding aggregations

2018
R Soc Open Sci
PMCID: 5792883
PMID: 29410806
DOI: 10.1098/rsos.170925
call_split See protocol

[…] er chance of a tree including informative variables (i.e. loci under selection) when the dataset has relatively few such variables. Missing data were imputed—which is a requirement of the analysis—in GENODIVE 2.0b27 [] by conservatively (i.e. expected to find fewer loci putatively under selection) drawing alleles from the allele frequency distribution of the entire dataset rather than for each fee […]

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

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