The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction.
The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction.
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DOI：
10.3897/bdj.2.e1053
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发表时间：
2014
影响因子：
1.3
通讯作者：
Davis KE
中科院分区：
文献类型：
--
作者：
Hill J;Davis KE
构建大型超级树涉及收集、存储和处理数千个个体的单基因，以创建具有数千至数万个分类群的大型单基因。这种大规模的遗传变异对于宏观进化研究、比较生物学以及生物多样性保护都是有用的。目前没有易于使用和完全集成的软件包来执行这项任务。在这里，我们提出了一个新的基于Python的软件包，使用定义良好的XML模式来管理数据和元数据。它建立在以前的版本上，1）包括新的处理步骤，如安全分类简化，2）使用用户友好的GUI，指导用户至少完成所需的最低信息，并包括上下文敏感的文档，3）修订的存储格式，将树和元数据集成到一个文件中。然后，可以使用GUI或基于命令行的工具，根据定义良好但灵活的处理管道来操作这些数据。处理步骤包括名称标准化、删除或替换分类群、确保充分的分类重叠、确保数据独立性和安全的分类简化。该软件已成功地用于存储和处理由1000多棵树组成的数据，这些树已准备好使用标准超树方法进行分析。该软件使创建大型超树变得更加容易，并为进一步的工作提供了更大的灵活性。
Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work.