用于操作Orthology数据的orthxml文件的工具包。

IF 1.8 3区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Evolution Pub Date : 2025-09-26 DOI:10.1007/s00239-025-10271-7

Ali Yazdizadeh Kharrazi, Adrian M Altenhoff, Nikolai Romashchenko, Christophe Dessimoz, Sina Majidian

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引用次数: 0

摘要

OrthoXML文件是用于正字学数据的标准文件格式。它提供了一个标准化的结构，用于描述同源和平行关系，同时允许用户以相同的格式存储自定义数据和特定于数据库的数据。尽管许多正字法数据库使用它作为导出数据的一种方式，但是没有用于处理这种格式的综合工具包。在这里，我们将介绍OrthoXML-tools (https://github.com/DessimozLab/orthoxml-tools)，这是一个用于加载、操作和将OrthoXML文件导出为其他格式的综合工具包。我们在基准测试中展示了它的能力和性能。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.

The OrthoXML file is a standard file format for orthology data. It provides a standardized structure for describing orthologous and paralogous relationships while allowing the user to store custom and database-specific data in the same format. Although many orthology databases use it as a way to export data, there is no comprehensive toolkit for working with this format. Here, we introduce the OrthoXML-tools ( https://github.com/DessimozLab/orthoxml-tools ), a comprehensive toolkit for loading, manipulating, and exporting the OrthoXML files to other formats. We show its capabilities and performance on our benchmarks.

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来源期刊

Journal of Molecular Evolution 生物-进化生物学

CiteScore

5.50

自引率

2.60%

发文量

审稿时长

3 months

期刊介绍： Journal of Molecular Evolution covers experimental, computational, and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features, from the initial formation of macromolecular systems through their evolution at the molecular level, the co-evolution of their functions in cellular and organismal systems, and their influence on organismal adaptation, speciation, and ecology. Topics addressed include the evolution of informational macromolecules and their relation to more complex levels of biological organization, including populations and taxa, as well as the molecular basis for the evolution of ecological interactions of species and the use of molecular data to infer fundamental processes in evolutionary ecology. This coverage accommodates such subfields as new genome sequences, comparative structural and functional genomics, population genetics, the molecular evolution of development, the evolution of gene regulation and gene interaction networks, and in vitro evolution of DNA and RNA, molecular evolutionary ecology, and the development of methods and theory that enable molecular evolutionary inference, including but not limited to, phylogenetic methods.