Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
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DOI：
10.1038/s41598-020-58356-1
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发表时间：
2020-02-03
影响因子：
4.6
通讯作者：
Chain, Patrick S. G.
中科院分区：
文献类型：
--
作者：
Shakya, Migun;Ahmed, Sanaa A.;Chain, Patrick S. G.
从大量针对相关病毒、细菌或真核生物的基因组测序项目中重建基因组的兴趣越来越大。为了便于为不同类型的项目构建标准化和强大的系统发育，我们开发了一个完整的生物信息学工作流程，其中包含一个基于网络的组件，用于从测序读数，草图组装或密切相关生物体的完整基因组进行系统发育和分子进化（PhaME）分析。此外，结合原始数据的能力，包括含有靶生物体的一些宏基因组样品（例如来自具有疑似感染原的临床样品），显示出在不需要预先组装的情况下对复杂样品内的生物体进行快速系统发育表征的前景。
There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.