Open Tree of Life Taxonomy

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 http://figshare.com/articles/Fungal_Classification_2015/1465038. Download location: https://github.com/OpenTreeOfLife/reference-taxonomy/tree/ott2.10draft11/feed/h2007

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: http://www.arb-silva.de/. Download location: ftp://ftp.arb-silva.de/release_115/Exports/tax_ranks_ssu_115.csv.

Index Fungorum. Download location: derived from database query result files provided by Paul Kirk, 7 April 2014 (personal communication). Web site: http://www.indexfungorum.org/. Download location (converted to OTT format): http://files.opentreeoflife.org/fung/fung-9/fung-9-ot.tgz.

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: http://purl.org/opentree/ott/ott2.8/inputs/lamiales-20140118.tsv

World Register of Marine Species (WoRMS) - harvested from web site using web API over several days ending around 1 October 2015. Download location: http://files.opentreeoflife.org/worms/worms-1/worms-1-ot.tgz

NCBI Taxonomy, from the US National Center on Biotechnology Information. Web site: http://www.ncbi.nlm.nih.gov/Taxonomy/. We used a version dated 16 September, 2019. Archived location: http://files.opentreeoflife.org/ncbi/ncbi-20190916/ncbi-20190916.tgz. Current version download location: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz

GBIF Backbone Taxonomy, from the Global Biodiversity Information facility. We used a version dated 2019-09-16. Download location: http://files.opentreeoflife.org/gbif/gbif-20190916/gbif-20190916.zip. Current version download location (unverified): http://rs.gbif.org/datasets/backbone/backbone-current.zip.

Interim Register of Marine and Nonmarine Genera (IRMNG). We used a version dated 2014-01-31. Download location: http://purl.org/opentree/ott/ott2.8/inputs/IRMNG_DWC-2014-01-30.zip.