National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4, Canada.
Bioinformatics. 2017 Nov 15;33(22):3638-3641. doi: 10.1093/bioinformatics/btx459.
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.
Phylotyper is a python and R package. It is available from: https://github.com/superphy/insilico-subtyping.
matthew.whiteside@phac-aspc.gc.ca.
Supplementary data are available at Bioinformatics online.
全基因组测序（WGS）正被应用于公共卫生领域，以改善监测和疫情分析。在公共卫生领域，亚型分析已被用于推断表型和区分细菌株群。需要能够从序列数据中预测亚型的计算机工具，以便将历史数据转换为基于 WGS 的方案。Phylotyper 是一种从基因序列预测亚型的新型计算工具。它专为纳入 WGS 管道而设计，是一种通用的预测工具，可应用于不同的亚型方案。Phylotyper 使用系统发育来模拟亚型的进化，并为未注释的序列推断亚型。Phylotyper 中的系统发育框架优于仅基于序列相似性的方法，可提供有用的上下文反馈。
Phylotyper 是一个 Python 和 R 包。它可从以下网址获得：https://github.com/superphy/insilico-subtyping。
matthew.whiteside@phac-aspc.gc.ca。
补充数据可在“Bioinformatics”在线获得。
