This app generates genotype-based and hierarchical nomenclature, akin to a simplified Pango-style naming schema. AutoLin iteratively generates labels, ensuring mutually exclusive lineage assignments based on user-defined conditions and proportions of samples. It seamlessly integrates with Auspice v2 format JSON files, ideally those containing mutation annotations and amino acid change translations. Users can easily upload the enhanced JSON files to Auspice for visualization.

See owner's GitHub repository for more information: https://github.com/jmcbroome/automated-lineage-json.

This work is based on the paper:

McBroome, J., Schneider, A. d. B., Roemer, C., Wolfinger, M. T., Hinrichs, A. S., O’Toole, A. N., Ruis, C., Turakhia, Y., Rambaut, A., & Corbett-Detig, R. (2023). Automated Agnostic Designation of Pathogen Lineages. bioRxiv, 2023.02.03.527052. https://doi.org/10.1101/2023.02.03.527052

This application was not uploaded by the author, but through their publicly available Github repository, https://github.com/jmcbroome/automated-lineage-json.