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. 2025 Sep 26.
doi: 10.1007/s00239-025-10271-7. Online ahead of print.

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

Ali Yazdizadeh Kharrazi  1 , Adrian M Altenhoff  2   3 , Nikolai Romashchenko  3   4 , Christophe Dessimoz  3   4 , Sina Majidian  5
Affiliations

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

Ali Yazdizadeh Kharrazi et al. J Mol Evol. .

Abstract

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.

Keywords: Comparative genomics; Hierarchical orthologous groups; OrthoXML; Orthology.

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