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

BMC Bioinformatics
Alexandre P FranciscoJoäo A Carriço

Abstract

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. 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. 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.p...Continue Reading

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Citations

Aug 22, 2012·Antimicrobial Agents and Chemotherapy·C Silva-CostaUNKNOWN Portuguese Group for the Study of Streptococcal Infections
Apr 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·Matteo De ChiaraClaudio Donati
Jun 25, 2014·Future Microbiology·Keith A Jolley, Martin C J Maiden
Sep 23, 2014·International Journal of Microbiology·Ann-Kristin Tveten
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Feb 5, 2013·Veterinary Microbiology·Shlomo E Blum, Gabriel Leitner
Dec 3, 2015·The Veterinary Journal·Inna LysnyanskySharon Levisohn
Dec 19, 2015·Research in Veterinary Science·S BarandiaranM J Zumárraga
Sep 6, 2015·International Journal of Medical Microbiology : IJMM·Sabrina JungnickVolker Fingerle
Aug 8, 2013·Environmental Microbiology·Maria Elena MartinoBarbara Cardazzo
Feb 27, 2016·International Journal of Medical Microbiology : IJMM·Ying-Chen WuTer-Hsin Chen
Dec 11, 2013·Journal of Medical Microbiology·Giuliano GarofoloElisabetta Di Giannatale
Jul 5, 2015·The Journal of Antimicrobial Chemotherapy·C Silva-CostaUNKNOWN Portuguese Group for the Study of Streptococcal Infections
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Jul 15, 2015·BMC Veterinary Research·Zsuzsanna RónaiMiklós Gyuranecz

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Software Mentioned

AbstractDistance
PHYLOViZ Seeking Mantra
PHYLOViZ Aligned Sequences
PHYLOViZ PubMLST
PHYLOViZ Category
Excel
EcMLST
PHYLOViZ LoadMLST
PHYLOViZ MLVA
PHYLOViZ SNP

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