PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods
Alexandre P. Francisco,Alexandre P. Francisco,Cátia Vaz,Pedro T. Monteiro,Pedro T. Monteiro,José Melo-Cristino,Mário Ramirez,João A. Carriço,João A. Carriço +8 more
TLDR
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.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.phyloviz.net
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GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens
Zhemin Zhou,Nabil-Fareed Alikhan,Martin J. Sergeant,Nina Luhmann,Cátia Vaz,Alexandre P. Francisco,Alexandre P. Francisco,João A. Carriço,Mark Achtman +8 more
TL;DR: GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.
Journal ArticleDOI
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
Joshua Quick,Philip Ashton,Szymon T. Calus,Carole Chatt,Savita Gossain,Jeremy Hawker,Satheesh Nair,Keith Neal,Kathy Nye,Tansy Peters,Elizabeth de Pinna,Esther Robinson,Keith Struthers,Mark A. Webber,Andrew Catto,Timothy J. Dallman,Peter M. Hawkey,Peter M. Hawkey,Nicholas J. Loman +18 more
TL;DR: This work investigated the potential of a newly released sequencing technology, the MinION from Oxford Nanopore Technologies, in the management of a hospital outbreak of Salmonella, and demonstrated that rapid MiSeq sequencing can reduce the time to answer compared to the standard sequencing protocol with no impact on the results.
Journal ArticleDOI
PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
Marta Nascimento,Marta Nascimento,Adriano Sousa,Mário Ramirez,Alexandre P. Francisco,Alexandre P. Francisco,João A. Carriço,Cátia Vaz,Cátia Vaz +8 more
TL;DR: PHYLOViZ 2.0 is presented, an extension of PHYLoviZ tool, a platform independent Java tool that allows phylogenetic inference and data visualization for large datasets of sequence based typing methods, including Single Nucleotide Polymorphism (SNP) and whole genome/core genome Multilocus Sequence Typing (wg/cgMLST) analysis.
Journal ArticleDOI
Pathogen typing in the genomics era: MLST and the future of molecular epidemiology.
Marcos Pérez-Losada,Patricia Cabezas,Patricia Cabezas,Eduardo Castro-Nallar,Keith A. Crandall +4 more
TL;DR: The literature is simply too vast to make this review comprehensive, nevertheless, it is attempted to include enough references in a variety of key areas to introduce the reader to the broad applications and complications of MLST data.
Posted ContentDOI
GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens
Zhemin Zhou,Nabil-Fareed Alikhan,Martin J. Sergeant,Nina Luhmann,Cátia Vaz,Alexandre P. Francisco,Alexandre P. Francisco,João A. Carriço,Mark Achtman +8 more
TL;DR: G GrapeTree implements a novel minimum spanning tree algorithm to reconstruct genetic relationships despite missing data together with a static “GrapeTree Layout” algorithm to render interactive visualisations of large trees.
References
More filters
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Performance standards for antimicrobial susceptibility testing
TL;DR: The supplemental information presented in this document is intended for use with the antimicrobial susceptibility testing procedures published in the following Clinical and Laboratory Standards Institute (CLSI)–approved standards.
Proceedings Article
Gephi: An Open Source Software for Exploring and Manipulating Networks
TL;DR: This work presents several key features of Gephi in the context of interactive exploration and interpretation of networks, and highlights key aspects of dynamic network visualization.
Proceedings ArticleDOI
The eyes have it: a task by data type taxonomy for information visualizations
TL;DR: A task by data type taxonomy with seven data types and seven tasks (overview, zoom, filter, details-on-demand, relate, history, and extracts) is offered.
Journal ArticleDOI
On the shortest spanning subtree of a graph and the traveling salesman problem
TL;DR: Kurosh and Levitzki as discussed by the authors, on the radical of a general ring and three problems concerning nil rings, Bull Amer Math Soc vol 49 (1943) pp 913-919 10 -, On the structure of algebraic algebras and related rings.