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Open Tree of Life Taxonomy

OpenTreeofLife; Karen A. Cranston; Benjamin Redelings; Luna Luisa Sanchez Reyes; Jim Allman; Emily Jane McTavish; Mark T. Holder

The reference taxonomy is an algorithmic combination of several source taxonomies. For code, see the source code repository. Version 3.2 draft 9 was generated using commit 618bab0ca3.

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  • Curated additions from the Open Tree amendments-1 repository, commit 12c810f5. These taxa are added during OTU mapping using the curator application.

  • Taxonomy from: DS Hibbett, M Binder, JF Bischoff, M Blackwell, et al. A higher-level phylogenetic classification of the Fungi. Mycological Research 111(5):509-547, 2007. Newick string with revisions archived at Download location:

  • Taxonomy from: SILVA 16S ribosomal RNA database, version 115. See: Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41 (D1): D590-D596. Web site: Download location:

  • Index Fungorum. Download location: derived from database query result files provided by Paul Kirk, 7 April 2014 (personal communication). Web site: Download location (converted to OTT format):

  • Taxonomy from: Schäferhoff, B., Fleischmann, A., Fischer, E., Albach, D. C., Borsch, T., Heubl, G., and Müller, K. F. (2010). Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences. BMC evolutionary biology 10(1), 352.. Manually transcribed from the paper and converted to OTT format. Download location:

  • World Register of Marine Species (WoRMS) - harvested from web site using web API over several days ending around 1 October 2015. Download location:

  • NCBI Taxonomy, from the US National Center on Biotechnology Information. Web site: We used a version dated 16 September, 2019. Archived location: Current version download location:

  • GBIF Backbone Taxonomy, from the Global Biodiversity Information facility. We used a version dated 2019-09-16. Download location: Current version download location (unverified):

  • Interim Register of Marine and Nonmarine Genera (IRMNG). We used a version dated 2014-01-31. Download location:

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