.png){kind=icon}
返回
Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)
.png){kind=icon}
OA
AI
DOI：10.1093/molbev/msz053.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
Subspecies nomenclature systems of pathogens are increasingly based on sequence data. The use of phylogenetics to identify and differentiate between clusters of genetically similar pathogens is particularly prevalent in virology from the nomenclature of human papillomaviruses to highly pathogenic avian influenza (HPAI) H5Nx viruses. These nomenclature systems rely on absolute genetic distance thresholds to define the maximum genetic divergence tolerated between viruses designated as closely related. However, the phylogenetic clustering methods used in these nomenclature systems are limited by the arbitrariness of setting intra and intercluster diversity thresholds. The lack of a consensus ground truth to define well-delineated, meaningful phylogenetic subpopulations amplifies the difficulties in identifying an informative distance threshold. Consequently, phylogenetic clustering often becomes an exploratory, ad hoc exercise. Phylogenetic Clustering by Linear Integer Programming (PhyCLIP) was developed to provide a statistically principled phylogenetic clustering framework that negates the need for an arbitrarily defined distance threshold. Using the pairwise patristic distance distributions of an input phylogeny, PhyCLIP parameterizes the intra and intercluster divergence limits as statistical bounds in an integer linear programming model which is subsequently optimized to cluster as many sequences as possible. When applied to the hemagglutinin phylogeny of HPAI H5Nx viruses, PhyCLIP was not only able to recapitulate the current WHO/OIE/FAO H5 nomenclature system but also further delineated informative higher resolution clusters that capture geographically distinct subpopulations of viruses. PhyCLIP is pathogen-agnostic and can be generalized to a wide variety of research questions concerning the identification of biologically informative clusters in pathogen phylogenies. PhyCLIP is freely available at http://github.com/alvinxhan/PhyCLIP, last accessed March 15, 2019.
Keyword:
phylogenetic clustering
molecular epidemiology
influenza
pathogen
nomenclature
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
IF:
5.3
论文数:
8.4K
被引数:
8.1W
机构
引用论文
The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada临床，人口统计学和危险因素对HIV传播率的影响: 加拿大不列颠哥伦比亚省基于人群的系统发育分析OAAI
OAAI分享收藏Identification of the progenitors of Indonesian and Vietnamese avian influenza A (H5N1) viruses from southern China.png)
JOURNAL OF VIROLOGYOAAI
JOURNAL OF VIROLOGYIF3.8
OAAI分享收藏Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study通过常规HIV基因分型对HIV传播热点进行近实时监测: 一项实施案例研究LANCET HIVOAAI
LANCET HIVIF13
OAAI分享收藏
查看更多内容