Genome-Based Taxonomic Classification of Bacteroidetes.

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Published in Front Microbiol on December 20, 2016

Authors

Richard L Hahnke1, Jan P Meier-Kolthoff1, Marina García-López1, Supratim Mukherjee2, Marcel Huntemann2, Natalia N Ivanova2, Tanja Woyke2, Nikos C Kyrpides3, Hans-Peter Klenk4, Markus Göker1

Author Affiliations

1: Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany.
2: Department of Energy Joint Genome Institute (DOE JGI) Walnut Creek, CA, USA.
3: Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA; Department of Biological Sciences, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia.
4: School of Biology, Newcastle University Newcastle upon Tyne, UK.

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Multiple sequence alignment using partial order graphs. Bioinformatics (2002) 13.70

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res (2011) 10.82

Studies on the Cytophagas. J Bacteriol (1940) 10.70

Natural relationship between bacteroides and flavobacteria. J Bacteriol (1985) 10.00

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Phylogenomics: the beginning of incongruence? Trends Genet (2006) 3.68

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