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BayeScan specifications


Unique identifier OMICS_33841
Name BayeScan
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes




No version available


  • person_outline Gerald Heckel

Publications for BayeScan

BayeScan citations


Complex signatures of genomic variation of two non model marine species in a homogeneous environment

BMC Genomics
PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y

[…] from 40 individually genotyped individuals. GenePop files were further edited using custom Perl script, to merge all contigs and identify locus positions.The edited GenePop files were converted into Bayescan files using PGDSpider2 v2.1.03 []. The first outlier detection method, Bayescan v.2.1 [], was run with 20 pilot runs, 10,000 iterations and a burn-in of 50,000, and 55,000 reversible-jump MCM […]


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

[…] ferent Bayesian approaches to detect SNPs deviating from neutral expectations and to assess the degree of correlations with environmental parameters. We employed the FST-based approach implemented in BayeScan v.2.1 [] to identify outlier loci. In order to test for associations between population genetic divergence and environmental parameters, we also employed two approaches implemented in BayeScE […]


Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana

Proc Natl Acad Sci U S A
PMCID: 5948977
PMID: 29686078
DOI: 10.1073/pnas.1719998115

[…] We used BayeScan2.0 () to estimate FST: a method that incorporates a multinomial Dirichlet likelihood () to account for variation in allele frequencies due to various neutral population genetic models. We use […]


Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral

PLoS Genet
PMCID: 5908067
PMID: 29672529
DOI: 10.1371/journal.pgen.1007220

[…] Prior to demographic analysis, Bayescan [] was used to identify sites potentially under selection among populations, and 73 sites with q-value <0.5 were removed. This aggressive removal of potential non-neutral sites resulted in be […]


Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

Ecol Evol
PMCID: 5938456
PMID: 29760905
DOI: 10.1002/ece3.4017
call_split See protocol

[…] l locus depths of 5 and 10, respectively). Conversion of file formats from STACKS output files was made using PGDSpider v. (Lischer & Excoffier, ). Possible outlier loci were identified using Bayescan v. 2.1 (Foll & Gaggiotti, ) with a burn‐in of 5 × 104 followed by a total of 1 × 106 iterations. Loci were determined to be under balancing or purifying selection when alpha values were zero […]


The ecology of immune state in a wild mammal, Mus musculus domesticus

PLoS Biol
PMCID: 5919074
PMID: 29652925
DOI: 10.1371/journal.pbio.2003538
call_split See protocol

[…] autosomal loci as described in []. In total, 445 mice were genotyped: 443 wild mice and 2 laboratory C57BL/6 mice (L88 female and L90 male), as in []. The neutrality of the loci was tested using the Bayescan program [], which detected 15 loci that were unlikely to be neutral and these were removed from further analyses, leaving data for 1,168 loci.We used Arlequin to calculate Hardy-Weinberg expe […]


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BayeScan institution(s)
Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland; Swiss Institute of Bioinformatics, Genopode, Lausanne, Switzerland
BayeScan funding source(s)
Supported by the University of Bern Research Foundation and the Swiss National Science Foundation (projects 3100A0-112072 and 3100-126074).

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