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PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

2012-05-08Journal article Open access
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dc.contributor.authorFrancisco, Alexandre P.
dc.contributor.authorVaz, Cátia
dc.contributor.authorMonteiro, Pedro T.
dc.contributor.authorMelo-Cristino, José
dc.contributor.authorRamirez, Mario
dc.contributor.authorCarrico, Joao
dc.date.accessioned2012-11-02T16:59:32Z
dc.date.available2012-11-02T16:59:32Z
dc.date.issued2012-05-08
dc.description.abstractBackground: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.por
dc.identifier.citationFRANCISCO, Alexandre P.; [et al] – PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics. ISSN 1471-2105. Vol. 13 (2012), pp. 1-10.por
dc.identifier.doi10.1186/1471-2105-13-87
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/10400.21/1877
dc.language.isoengpor
dc.peerreviewedyespor
dc.publisherBiomed Central LTDpor
dc.subjectSalmonella-Typhipor
dc.subjectEvolutionpor
dc.subjectNetworkspor
dc.subjectMutationspor
dc.titlePHYLOViZ: phylogenetic inference and data visualization for sequence based typing methodspor
dc.typejournal article
dspace.entity.typePublication
oaire.citation.conferencePlaceLondonpor
oaire.citation.endPage10
oaire.citation.startPage1
oaire.citation.titleBMC Bioinformaticspor
oaire.citation.volume13por
person.familyNameVaz
person.familyNameCarrico
person.givenNameCátia
person.givenNameJoao
person.identifier.ciencia-id8718-741E-BBD9
person.identifier.orcid0000-0001-6074-3074
person.identifier.orcid0000-0002-5274-2722
person.identifier.ridADC-1473-2022
person.identifier.ridA-7367-2008
person.identifier.scopus-author-id27267941600
person.identifier.scopus-author-id8266333200
rcaap.rightsrestrictedAccesspor
rcaap.typearticlepor
relation.isAuthorOfPublication0c5cb0fd-7cd7-4a16-86a8-7a68188e53ff
relation.isAuthorOfPublication5f4ad9ce-0a68-496f-a0d6-2062d39f4702
relation.isAuthorOfPublication.latestForDiscovery5f4ad9ce-0a68-496f-a0d6-2062d39f4702

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