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Bayenv specifications


Unique identifier OMICS_05827
Name Bayenv
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publications for Bayenv

Bayenv citations


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

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

[…] ] to identify outlier loci. In order to test for associations between population genetic divergence and environmental parameters, we also employed two approaches implemented in BayeScEnv v.1.1 [] and BayEnv v.2 []. Details of the estimations are listed in Additional file . In addition, allele frequencies were plotted for outlier loci in order to assess the spatial cline. […]


Navigating the Interface Between Landscape Genetics and Landscape Genomics

Front Genet
PMCID: 5859105
PMID: 29593776
DOI: 10.3389/fgene.2018.00068

[…] ), and XTX, which employs a Bayesian method to test individual SNPs against a null model generated by the covariance in allele frequencies between populations from the entire set of SNPs (utilized in Bayenv2; Coop et al., ; Günther and Coop, ). Summaries of differentiation outlier methods can be found in Hoban et al. (; Appendix 1). Notably, differentiation outlier methods are aspatial in nature.G […]


Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus

Ecol Evol
PMCID: 5838053
PMID: 29531698
DOI: 10.1002/ece3.3846

[…] We used two separate methods to detect outlier loci using both environmental datasets (four tests in total). The first method used a Bayesian framework implemented in the program BAYENV2 (Coop, Witonsky, Di Rienzo, & Pritchard, ; Guenther & Coop, ). This method calculates a set of “standardized allele frequencies” that controls for population history and structure when detecti […]


Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks

PLoS One
PMCID: 5805252
PMID: 29420661
DOI: 10.1371/journal.pone.0192062

[…] enes potentially affected by directional and balancing selection, respectively. A further test of differentiation by selection was conducted with BayPass v2.1 [] which is a fast implementation of the Bayenv2 algorithm []. We first estimated the population covariance matrix Ω, which is a variance-covariance matrix of allele frequencies, for the two groups of accessions from each genebank was calcul […]


Ten Years of Landscape Genomics: Challenges and Opportunities

Front Plant Sci
PMCID: 5733015
PMID: 29312391
DOI: 10.3389/fpls.2017.02136

[…] models (; ) and canonical correlations and multivariate linear regressions, e.g., CCA (; ) and RDA (; ). A fifth important category of statistical methods comprises the mixed effects models, such as BAYENV (), LFMMs (), TASSEL (), and EMMA (). These approaches provide a unified statistical framework for controlling for the effects of neutral genetic structure (). For example, BAYENV, based on a B […]


RAD Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially Varying Selection in the American Eel (Anguilla rostrata)

Genome Biol Evol
PMCID: 5714190
PMID: 29136139
DOI: 10.1093/gbe/evx226

[…] A total of 90 SNPs detected as candidate outliers with Bayenv2 were retained for further downstream analyses (, online). Among these, 15 outlier markers were associated with the latitude of the sampling site, 16 to the longitude (among which four were al […]


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Bayenv institution(s)
Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, Stuttgart, Germany

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