BURST protocols

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BURST statistics

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BURST specifications

Information


Unique identifier OMICS_23753
Name BURST
Alternative names eBURST, goeBURST
Interface Web user interface
Restrictions to use None
Input data TSV
Output data A radial diagram.
Programming languages Java
Computer skills Basic
Version 3
Stability Stable
Maintained Yes

Maintainers


  • person_outline Alexandre Francisco <>
  • person_outline Miguel Bugalho <>
  • person_outline Mario Ramirez <>
  • person_outline Joao Carriço <>

Additional information


http://eburst.mlst.net/v3/instructions/ http://www.phyloviz.net/goeburst/#Software

Information


Unique identifier OMICS_23753
Name BURST
Alternative names eBURST, goeBURST
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.2.1
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Alexandre Francisco <>
  • person_outline Miguel Bugalho <>
  • person_outline Mario Ramirez <>
  • person_outline Joao Carriço <>

Additional information


http://eburst.mlst.net/v3/instructions/ http://www.phyloviz.net/goeburst/#Software

Publications for BURST

BURST in pipelines

 (53)
2018
PMCID: 5764299
PMID: 29386908
DOI: 10.2147/IDR.S152162

[…] of nucleotides, and the nonsynonymous/synonymous ratio (dn/ds) were calculated., mlst allelic profiles were analyzed to examine the relationship within the sts of the 160 clinical isolates using eburst v3, available from http://eburst.mlst.net/. isolates with five or more identical alleles were considered as part of the same clonal complexes (ccs)., for sequence-based phylogenetic tree […]

2018
PMCID: 5880904
PMID: 29636749
DOI: 10.3389/fmicb.2018.00592

[…] archive under the bioproject prjna315192. short read archive accession numbers are available in supplementary table ., serovars were inferred from the sequencing data using the seven-gene mlst and eburst group approach (; ). traditional serotyping was not performed., for the identification of amr determinants, the ‘genefinder’ algorithm was employed, which maps the sequencing reads to a set […]

2018
PMCID: 5893783
PMID: 29670859
DOI: 10.3389/fcimb.2018.00097

[…] included data from 11927 isolates (with sequence type – st, attributed), from 63 countries, representing 2467 distinct sts, at the time this analysis was conducted (17.10.2017). the eburst algorithm (francisco et al., ) implemented in the phyloviz2.0 software (nascimento et al., ) was used to construct a full minimum spanning tree (mst) displaying the relationships […]

2017
PMCID: 5242430
PMID: 28099434
DOI: 10.1371/journal.pntd.0005223

[…] patterns of evolutionary descent among genotypes according to their source and geographic region, the allelic profile of the southeastern brazilian and the global dataset were applied to the goeburst algorithm in philoviz software available at http://www.phyloviz.net/wiki/ []. in this analysis, differences between sts are presented as single locus variant (slv), double locus variant […]

2017
PMCID: 5400095
PMID: 28065889
DOI: 10.1093/jac/dkw559

[…] sample size (ess) was >200. posterior probabilities were calculated with a 10% burn-in and values >0.7 were considered significant. results were visualized in figtree (v. 1.40). additionally, goeburst (v 1.2.1) software was used for population structure analysis of sts. analysis was conducted at double- and triple-locus variant levels. single- and double-locus variants of previously […]


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BURST in publications

 (587)
PMCID: 5944035
PMID: 29743119
DOI: 10.1186/s13062-018-0211-z

[…] [, ]., the phylogenetic trees were built with raxml [] version 8.1.15 (parameters: -p 1989 -m gtrcat) and plotted with graphlan []. minimum spanning trees were drawn with phyloviz 2 [] using the goeburst full mst algorithm []. the principal component analysis (pca) plots were drawn with the scikit-learn package using the aligned concatenated markers sequences of strainphlan as arrays […]

PMCID: 5934806
PMID: 29724185
DOI: 10.1186/s12879-018-3114-9

[…] typing. capsular polysaccharide synthesis genes and other virulence factors were examined using multiplex pcr. diversity was calculated using divein, clonal relationship was determined using eburst, and phylogenetic analysis was performed using splitstree4., a polyclonal oxa-48 gene alone was the most common carbapenemase detected in 48/71 (67.6%) isolates followed by ndm-1 alone in 9/71 […]

PMCID: 5928140
PMID: 29740480
DOI: 10.3389/fgene.2018.00148

[…] complexes (ccs), singletons present, and the relationship between established groups; a preliminary step in describing the population structure of cryptococcus complex members was applied with the eburst v3 package, using as the input the allelic profiles for each species. burst is directed to the analysis of closely related sequences connected by changes in unique nucleotides, and therefore […]

PMCID: 5908911
PMID: 29674708
DOI: 10.1038/s41598-018-24708-1

[…] for each variable was calculated using the hunter gaston index with the vdice online tool (http://www.hpa-bioinformatics.org.uk/cgi-bin/dici/dici.pl)., minimum spanning trees (mst) were created by goeburst implemented in phyloviz. sts were represented by circles; the size of a circle indicates the number of isolates of this particular st. two approaches were performed: conventional mst using […]

PMCID: 5908202
PMID: 29630632
DOI: 10.1371/journal.pntd.0006379

[…] isolates using an abi prism 3130 genetic analyzer (applied biosystems) was performed using six vntrs as described previously [], and the relationship between the isolates was established using the goeburst algorithm on phyloviz v1.1 (http://www.phyloviz.net/). we performed a phylogenetic assessment of the core v. cholerae genome of the strains of the third wave of the seventh pandemic [] based […]


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BURST institution(s)
Instituto de Engenharia de Sistemas e Computadores – ID em Lisboa, Lisboa, Portugal; Instituto Superior Técnico, Universidade Técnica de Lisboa, Lisboa, Portugal; Instituto de Microbiologia/Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
BURST funding source(s)
Supported, in part, by Fundação para a Ciência e a Tecnologia (SFRH/BD/13215/2003) and, in part, by Fundação para a Ciência e a Tecnologia (PTDC/SAU-ESA/71499/2006).

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