BACKGROUND Phylogenetic 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. RESULTS Here, 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. CONCLUSIONS Together 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).

中文翻译：

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PhySpeTree：用于重建系统发育树的自动化管道。

背景技术系统发生树被广泛用于推断进化关系。现有的软件和算法主要集中在系统发生推理上。但是，对中间步骤的关注较少，例如处理非常大的序列以及准备配置文件以连接多个软件。当树种数量很大时，中间步骤将成为瓶颈，可能会严重影响树木的建造效率。结果在这里，我们提出了一个名为PhySpeTree的易于使用的管道，以促进细菌，古细菌和真核生物之间物种树的重建。用户只需要输入物种名称的缩写即可；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，清理序列并构建树。PhySpeTree允许用户通过调整高级选项执行关键步骤，例如序列比对和树构建。PhySpeTree提供了两个分别基于串联的高度保守的蛋白质和小的亚基核糖体RNA序列的平行管线。附件模块（例如用于插入新物种，生成可视化配置和合并树木的模块）与PhySpeTree一起分发。结论PhySpeTree与附件模块一起极大地简化了树的重建。PhySpeTree是在现代操作系统（Linux，macOS和Windows）上运行的Python中实现的。源代码可通过详细文档（https://github.com/yangfangs/physpetools）免费获得。