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<p>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 (<a href="https://github.com/DessimozLab/orthoxml-tools">https://github.com/DessimozLab/orthoxml-tools</a>), a comprehensive toolkit for loading, manipulating, and exporting the OrthoXML files to other formats. We show its capabilities and performance on our benchmarks.</p>

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

  • 期刊论文

  • 发表日期：

    2025年9月26日

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

摘要

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.