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BAPS specifications


Unique identifier OMICS_11072
Alternative name Bayesian Analysis of Population Structure
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 6.0
Stability Stable
Maintained Yes


No version available



  • person_outline Jukka Corander

Publications for Bayesian Analysis of Population Structure

BAPS citations


Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Wellcome Open Res
PMCID: 5930550
PMID: 29774245
DOI: 10.21956/wellcomeopenres.15526.r32391

[…] c ), several clonal groups within each lineage, long branches and a polyphyletic population cluster. Population clusters were estimated from the resulting core genome alignment from simulations using Bayesian Analysis of Population Structure v6.0 (BAPS) . We define N as the number of strains in the study and M as the number of aligned sites.We used realistic parameters, as far as possible, for the […]


Spatial genetic diversity in the Cape mole rat, Georychus capensis: Extreme isolation of populations in a subterranean environment

PLoS One
PMCID: 5854370
PMID: 29543917
DOI: 10.1371/journal.pone.0194165

[…] an interpolation-based graphic approach in the programme Alleles In Space []. To investigate the genetic clustering of individuals across the range of Georychus, clustering analyses were performed in BAPS version 6.0 [, , ] by employing both a normal clustering search (without geographic data) and a spatial clustering search (using the coordinates of sampled localities). […]


Molecular Evidences of a Hidden Complex Scenario in Leporinus cf. friderici

Front Genet
PMCID: 5818402
PMID: 29497440
DOI: 10.3389/fgene.2018.00047
call_split See protocol

[…] nd a HKY substitution model chosen by jModeltest 2 (). A total of 50 million MCMC generations and a burn-in of 10% were used. In second, a Bayesian analysis of genetic structure was implemented using BAPS software (). The maximum number of genetically diverged groups (K) was firstly set up for 10 replicates, 10 times. The obtained groups containing samples from different basins were submitted to a […]


Candidate gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae

Sci Rep
PMCID: 5811533
PMID: 29440767
DOI: 10.1038/s41598-018-21265-5

[…] expected heterozygosities, and to test for deviation from Hardy-Weinberg expectations. Individual cluster analysis of genotypes at the control (intergenic and non-candidate) SNP loci was performed by BAPS 5.2,, with multiple runs performed to obtain the optimum clustering solution. […]


Genetic Pattern and Demographic History of Salminus brasiliensis: Population Expansion in the Pantanal Region during the Pleistocene

Front Genet
PMCID: 5776086
PMID: 29387083
DOI: 10.3389/fgene.2018.00001

[…] lysis with Reticulate Trees – ).We investigated whether there were distinct mitochondrial genetic clusters by assigning individuals to populations using a Bayesian model-based approach implemented in Bayesian Analysis of Population Structure (BAPS) v. 6.0 (). BAPS identifies clusters based on nucleotide frequencies in DNA sequences. We concatenated mitochondrial markers and conducted a mixing anal […]


Phylogeographic analyses of the pampas cat (Leopardus colocola; Carnivora, Felidae) reveal a complex demographic history

Genet Mol Biol
PMCID: 5913729
PMID: 29668017
DOI: 10.1590/1678-4685-GMB-2017-0079

[…] ous studies of this species (; ; ). Several monophyletic clusters were identified in the phylogenetic analyses, in strong concordance with the groups found by for the central Andes. According to the BAPS analyses, these clusters could be joined into five main genetic groups distributed in west-east and north-south directions. However, these lineages were not completely allopatric, given the co-oc […]


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BAPS institution(s)
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland; Cardiff School of Biosciences, Cardiff University, Cardiff, UK; Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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