Bibliography

BGS+16

Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel J. P. Douzery, and Fabio Pardi. Fast and accurate branch lengths estimation for phylogenomic trees. BMC Bioinformatics, 17(1):23, December 2016. doi:10.1186/s12859-015-0821-8.

GlocknerYQ+17

Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati, Andreea Ciuprina, Gerrit Bruns, Pablo Yarza, Jörg Peplies, Ralf Westram, and Wolfgang Ludwig. 25 years of serving the community with ribosomal RNA gene reference databases and tools. Journal of Biotechnology, 261:169–176, November 2017. doi:10.1016/j.jbiotec.2017.06.1198.

MPG+12

Daniel McDonald, Morgan N. Price, Julia Goodrich, Eric P. Nawrocki, Todd Z. DeSantis, Alexander Probst, Gary L. Andersen, Rob Knight, and Philip Hugenholtz. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME Journal, 6(3):610–618, March 2012. doi:10.1038/ismej.2011.139.

NLT+19

Rolf Henrik Nilsson, Karl-Henrik Larsson, Andy F S Taylor, Johan Bengtsson-Palme, Thomas S Jeppesen, Dmitry Schigel, Peter Kennedy, Kathryn Picard, Frank Oliver Glöckner, Leho Tedersoo, Irja Saar, Urmas Kõljalg, and Kessy Abarenkov. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47(D1):D259–D264, January 2019. doi:10.1093/nar/gky1022.

PCC+20

Donovan H. Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J. Mussig, and Philip Hugenholtz. A complete domain-to-species taxonomy for Bacteria and Archaea. Nature Biotechnology, 38(9):1079–1086, September 2020. doi:10.1038/s41587-020-0501-8.

PDA10

Morgan N. Price, Paramvir S. Dehal, and Adam P. Arkin. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3):e9490, March 2010. doi:10.1371/journal.pone.0009490.

RC17

Jonathan Rees and Karen Cranston. Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal, 5:e12581, May 2017. doi:10.3897/BDJ.5.e12581.

SEOK96

Gregory D. Schuler, Jonathan A. Epstein, Hitomi Ohkawa, and Jonathan A. Kans. [10] Entrez: Molecular biology database and retrieval system. In Methods in Enzymology, volume 266 of Computer Methods for Macromolecular Sequence Analysis, pages 141–162. Academic Press, January 1996. doi:10.1016/S0076-6879(96)66012-1.