{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T07:09:13Z","timestamp":1761808153718},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2017,7,18]],"date-time":"2017-07-18T00:00:00Z","timestamp":1500336000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Whole genome sequencing (WGS) is being adopted in public health for improved surveillance and outbreak analysis. In public health, subtyping has been used to infer phenotypes and distinguish bacterial strain groups. In silico tools that predict subtypes from sequences data are needed to transition historical data to WGS-based protocols. Phylotyper is a novel solution for in silico subtype prediction from gene sequences. Designed for incorporation into WGS pipelines, it is a general prediction tool that can be applied to different subtype schemes. Phylotyper uses phylogeny to model the evolution of the subtype and infer subtypes for unannotated sequences. The phylogenic framework in Phylotyper improves accuracy over approaches based solely on sequence similarity and provides useful contextual feedback.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Phylotyper is a python and R package. It is available from: https:\/\/github.com\/superphy\/insilico-subtyping.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx459","type":"journal-article","created":{"date-parts":[[2017,7,17]],"date-time":"2017-07-17T19:13:37Z","timestamp":1500318817000},"page":"3638-3641","source":"Crossref","is-referenced-by-count":5,"title":["Phylotyper: <i>in silico<\/i> predictor of gene subtypes"],"prefix":"10.1093","volume":"33","author":[{"given":"Matthew D","family":"Whiteside","sequence":"first","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor P J","family":"Gannon","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chad R","family":"Laing","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,7,18]]},"reference":[{"key":"2023051308380187700_btx459-B1","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051308380187700_btx459-B2","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.4315\/0362-028X.JFP-16-228","article-title":"Comparative evaluation of genomic and laboratory approaches for determination of Shiga toxin subtypes in Escherichia coli","volume":"79","author":"Carrillo","year":"2016","journal-title":"J. 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