PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees
PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees
复制标题
PhySpeTree：用于重建系统发育物种树的自动化管道
DOI：
10.1186/s12862-019-1541-x
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发表时间：
2019-12-02
影响因子：
3.4
通讯作者：
Niu，Yulong
中科院分区：
文献类型：
--
作者：
Fang，Yang;Liu，Chengcheng;Niu，Yulong
研究背景系统发生种树被广泛应用于物种进化关系的推断。现有的软件和算法主要集中在系统发育推理。但是，对中间步骤的关注较少，例如处理非常大的序列和准备配置文件以连接多个软件。当物种数量是大的，中间步骤成为一个瓶颈，可能会严重影响树building.ResultsHere的效率，我们提出了一个易于使用的管道命名为PhySpeTree，以方便重建的物种树跨越细菌，古细菌和真核生物。用户只需要输入物种名称的缩写; PhySpeTree为不同的软件准备复杂的配置文件，然后自动下载基因组数据，清理序列，并建立树。PhySpeTree允许用户通过调整高级选项来执行关键步骤，如序列比对和树构建。PhySpeTree提供了两个平行的管道，分别基于串联的高度保守的蛋白质和小亚基核糖体RNA序列。辅助模块，例如用于插入新物种、生成可视化配置和组合树木的模块，沿着PhySpeTree一起分发。结论与辅助模块一起，PhySpeTree显着简化了树木重建。PhySpeTree是在现代操作系统（Linux，macOS和Windows）上运行的Python中实现的。源代码和详细的文档（https：//github.com/yangfangs/physpetools）可以免费获得。
BackgroundPhylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building.ResultsHere, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree.ConclusionsTogether with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).