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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data
Ali Yazdizadeh Kharrazi1, Adrian M Altenhoff2,3, Nikolai Romashchenko3,4
1DataChef, The Hague, The Netherlands.
None:
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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