Bayenv specifications

Information


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

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Publication for Bayenv

Bayenv in publications

 (35)
PMCID: 5859105
PMID: 29593776
DOI: 10.3389/fgene.2018.00068

[…] ). software names include: geneland (guillot et al., ), structure (pritchard et al., ), tess (durand et al., ), popgraph (dyer and nason, ); bayescan foll and gaggiotti, , flk (bonhomme et al., ), bayenv2 (günther and coop, ), pcadapt (duforet-frebourg et al., ) faststructure (raj et al., ), admixture (alexander et al., ), tess3 (caye et al., )., indicates methods not yet widely used but show […]

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

[…] trophic levels., 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 […]

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

[…] 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 […]

PMCID: 5714190
PMID: 29136139
DOI: 10.1093/gbe/evx226

[…] extent to which genetic variation at outlier loci was explained by each explanatory variable., in order to detect outlier loci possibly influenced by spatially-varying selection, we used the program bayenv2 (; ) which searches for exceptional correlations between explanatory variables and allele frequencies at individual locus. although this method specifically takes into account the underlying […]

PMCID: 5696417
PMID: 29187979
DOI: 10.1002/ece3.3466

[…] scans for selection (tajima's d), subpopulation differentiation (xtx), and environmental association analyses with eleven climate variables carried out with two different methods (lfmm and bayenv2) identified genes putatively involved in local adaptation. interestingly, many of these genes were also identified as adaptation candidates in another poplar species, populus trichocarpa, […]


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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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