BAPS pipeline

BAPS specifications

Information


Unique identifier OMICS_11072
Name BAPS
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

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Documentation


Maintainer


  • person_outline Jukka Corander <>

Publications for Bayesian Analysis of Population Structure

BAPS IN pipelines

 (12)
2017
PMCID: 5241397
PMID: 28096486
DOI: 10.1128/mBio.01984-16

[…] statistics were employed to test the associations between the presence or absence of pneumococcal ogs and 30-day mortality, conditional on the bacterial population substructure as proposed by bayesian analysis of population structure (baps; analysis 11). all associations were determined using plink (39). candidate ogs were selected based on an association test with a p of <0.05 (with […]

2017
PMCID: 5241397
PMID: 28096486
DOI: 10.1128/mBio.01984-16

[…] associations between the presence or absence of pneumococcal ogs and 30-day mortality, conditional on the bacterial population substructure as proposed by bayesian analysis of population structure (baps; analysis 11). all associations were determined using plink (39). candidate ogs were selected based on an association test with a p of <0.05 (with bonferroni adjustment for multiple testing). […]

2017
PMCID: 5381664
PMID: 28137745
DOI: 10.1093/gbe/evx003

[…] of the hospital supplying the sample. the administrative borders of countries were obtained from the global administrative unit layers dataset of fao., evidence for recombination between different baps-clusters was assessed using several methods as studies show that no single method is optimal, whereas multiple approaches may maximize the chances of detecting recombination events (posada […]

2017
PMCID: 5550751
PMID: 28790205
DOI: 10.1128/mBio.00822-17

[…] were obtained from genbank. a maximum-likelihood (ml) phylogenetic tree based on the core genome was constructed by phyml, and population structure was determined by the bayesian clustering method (bayesian analysis of population structure [baps]). similar methods were used to analyze the population structure of the whole b. cereus group on the basis of the genomes of the 140 b. thuringiensis […]

2017
PMCID: 5550751
PMID: 28790205
DOI: 10.1128/mBio.00822-17

[…] elihood (ml) phylogenetic tree based on the core genome was constructed by phyml, and population structure was determined by the bayesian clustering method (bayesian analysis of population structure [baps]). similar methods were used to analyze the population structure of the whole b. cereus group on the basis of the genomes of the 140 b. thuringiensis and 152 other strains in this group., b. thur […]

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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