Abstract
High-throughput sequencing methods generated allele and single nucleotide polymorphism information for thousands of bacterial strains that are publicly available in online repositories and created the possibility of generating similar information for hundreds to thousands of strains more in a single study. Minimum spanning tree analysis of allelic data offers a scalable and reproducible methodological alternative to traditional phylogenetic inference approaches, useful in epidemiological investigations and population studies of bacterial pathogens. PHYLOViZ Online was developed to allow users to do these analyses without software installation and to enable easy accessing and sharing of data and analyses results from any Internet enabled computer. PHYLOViZ Online also offers a RESTful API for programmatic access to data and algorithms, allowing it to be seamlessly integrated into any third party web service or software. PHYLOViZ Online is freely available at https://online.phyloviz.net.
Highlights
High-throughput sequencing methods gave rise to a paradigm shift in microbial typing and genomic population structure studies [1,2]
Single Nucleotide Polymorphism (SNPs) analysis and whole or core genome MultiLocus Sequence Typing [3], result in profiles that have thousands of loci which can be used for outbreak investigation, epidemiological surveillance of clones of interest and bacterial population or evolutionary studies
The interactive displays of information, where the user can quickly switch between the combinations of parameters being represented, allows for the kind of analytical reasoning proposed by the visual analytics agenda [7]
Summary
High-throughput sequencing methods gave rise to a paradigm shift in microbial typing and genomic population structure studies [1,2]. With the aim of overcoming these limitations, PHYLOViZ Online was developed as a user-friendly web application for profile-based data analysis, visualization and sharing, allowing the application of visual Users can provide a file with auxiliary data in tabdelimited format to be represented onto the tree, such as demographic, temporal or epidemiological information, including antibiotic resistance or typing information from other methods.
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