title: PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees.
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.
authors.affiliation: Instituto de Microbiologia and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal bfgoncalves@medicina.ulisboa.pt.
authors.forename: Bruno
authors.identifier: 0000-0002-5775-6955
authors.initials: B
authors.lastname: Ribeiro-Gonçalves
authors.affiliation: INESC-ID / Instituto Superior Técnico, Universidade de Lisboa, 1000-029 Lisboa, Portugal.
authors.forename: Alexandre P
authors.identifier: 0000-0003-4852-1641
authors.initials: AP
authors.lastname: Francisco
authors.affiliation: INESC-ID / Instituto Superior Técnico, Universidade de Lisboa, 1000-029 Lisboa, Portugal Instituto Politécnico de Lisboa, 1959-007 Lisboa, Portugal.
authors.forename: Cátia
authors.initials: C
authors.lastname: Vaz
authors.affiliation: Instituto de Microbiologia and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
authors.forename: Mário
authors.identifier: 0000-0002-4084-6233
authors.initials: M
authors.lastname: Ramirez
authors.affiliation: Instituto de Microbiologia and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal jcarrico@medicina.ulisboa.pt.
authors.forename: João André
authors.identifier: 0000-0002-5274-2722
authors.initials: JA
authors.lastname: Carriço
mesh_terms: D000465:Algorithms; D000483:Alleles; D003196:Computer Graphics; D030541:Databases, Genetic; D066264:Datasets as Topic; D059014:High-Throughput Nucleotide Sequencing; D033181:Information Dissemination; D016247:Information Storage and Retrieval; D020407:Internet; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D065288:Serogroup; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics; D014584:User-Computer Interface