PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
复制标题
PhyloSuite：一个集成且可扩展的桌面平台，用于简化分子序列数据管理和进化系统发育学研究
DOI：
10.1111/1755-0998.13096
复制
发表时间：
2019-11-06
影响因子：
7.7
通讯作者：
Wang, Gui T.
中科院分区：
文献类型：
--
作者：
Zhang, Dong;Gao, Fangluan;Wang, Gui T.
多基因和基因组数据集在遗传学领域已经变得司空见惯，但是许多现有的工具不是针对这样的数据集而设计的，这通常使得分析耗时且繁琐。在这里，我们介绍了PhyloSuite，一个（跨平台，开源，独立的Python图形用户界面）用户友好的工作流程桌面平台，致力于简化分子序列数据管理和进化遗传学研究。它使用一个基于插件的系统，集成了几个系统发育和生物信息学工具，从而简化了整个过程，从数据采集到系统发育树注释（结合iTOL）。它具有以下特点：（a）点击和拖放图形用户界面;（B）管理和组织分子序列数据和分析结果的工作区;（c）GenBank条目提取和比较统计;和（d）具有批处理能力的系统发生工作流程，包括序列比对（mafft和macse），对齐优化（trimAl、HmmCleaner和Gblocks）、数据集拼接、最佳分割方案和最佳进化模型选择（分区和modelfinder），和系统发育推断（MrBayes和iq树）。PhyloSuite专为初学者和有经验的研究人员设计，允许前者快速启动系统发育分析，后者以简化的方式进行，存储和管理他们的工作，并花更多的时间研究科学问题，而不是浪费在将文件从一个软件程序传输到另一个软件程序上。
Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.