TY - JOUR AU - Woese, C. R. AU - Kandler, O. AU - Wheelis, M. L. PY - 1990 DA - 1990// TI - Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya JO - Proc Natl Acad Sci USA VL - 87 UR - https://doi.org/10.1073/pnas.87.12.4576 DO - 10.1073/pnas.87.12.4576 ID - Woese1990 ER - TY - JOUR AU - Wayne, L. G. AU - Brenner, D. J. AU - Colwell, R. R. AU - Grimont, P. A. D. AU - Kandler, O. AU - Krichevsky, M. I. AU - Moore, L. H. AU - Moore, W. E. C. AU - Murray, R. G. E. AU - Stackebrandt, E. PY - 1987 DA - 1987// TI - Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics JO - Int J Syst Bacteriol VL - 37 UR - https://doi.org/10.1099/00207713-37-4-463 DO - 10.1099/00207713-37-4-463 ID - Wayne1987 ER - TY - STD TI - Schleifer KH. Classification of Bacteria and Archaea: Past, present and future. Syst Appl Microbiol (In press). ID - ref3 ER - TY - JOUR AU - Tindall, B. J. AU - Rossello-Mora, R. AU - Busse, H. J. AU - Ludwig, W. AU - Kämpfer, P. PY - 2010 DA - 2010// TI - Notes on the characterization of prokaryote strains for taxonomic purposes JO - Int J Syst Evol Microbiol VL - 60 UR - https://doi.org/10.1099/ijs.0.016949-0 DO - 10.1099/ijs.0.016949-0 ID - Tindall2010 ER - TY - JOUR AU - Brenner, D. J. PY - 1973 DA - 1973// TI - Deoxyribonucleic acid reassociation in the taxonomy of enteric Bacteria JO - Int J Syst Bacteriol VL - 23 UR - https://doi.org/10.1099/00207713-23-4-298 DO - 10.1099/00207713-23-4-298 ID - Brenner1973 ER - TY - JOUR AU - Ley, J. PY - 1970 DA - 1970// TI - Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleotide acid JO - J Bacteriol VL - 101 ID - Ley1970 ER - TY - JOUR AU - Johnson, J. L. PY - 1973 DA - 1973// TI - Use of nucleic-acid homologies in the taxonomy of anaerobic Bacteria JO - Int J Syst Bacteriol VL - 23 UR - https://doi.org/10.1099/00207713-23-4-308 DO - 10.1099/00207713-23-4-308 ID - Johnson1973 ER - TY - CHAP AU - Rossello-Mora, R. ED - Stackebrandt, E. PY - 2006 DA - 2006// TI - DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation BT - Molecular Identification, Systematics and Population Structure of Prokaryotes PB - Springer CY - Berlin UR - https://doi.org/10.1007/978-3-540-31292-5_2 DO - 10.1007/978-3-540-31292-5_2 ID - Rossello-Mora2006 ER - TY - CHAP AU - Johnson, J. L. AU - Whitman, W. B. ED - Reddy, C. A. PY - 2007 DA - 2007// TI - Similarity analysis of DNAs BT - Methods for general and molecular microbiology PB - ASM Press CY - Washington D.C. ID - Johnson2007 ER - TY - JOUR AU - Elahi, E. AU - Ronaghi, M. PY - 2004 DA - 2004// TI - Pyrosequencing: a tool for DNA sequencing analysis JO - Methods Mol Biol VL - 255 ID - Elahi2004 ER - TY - JOUR AU - Ley, J. AU - Smedt, J. PY - 1975 DA - 1975// TI - Improvements of the membrane filter method for DNA:rRNA hybridization JO - Antonie Van Leeuwenhoek VL - 41 UR - https://doi.org/10.1007/BF02565064 DO - 10.1007/BF02565064 ID - Ley1975 ER - TY - JOUR AU - Klenk, H. P. AU - Haas, B. AU - Schwass, V. AU - Zillig, W. PY - 1986 DA - 1986// TI - Hybridization homology: A new parameter for the analysis of phylogenetic relations, demonstrated with the urkingdom of the archaebacteria JO - J Mol Evol VL - 24 UR - https://doi.org/10.1007/BF02099964 DO - 10.1007/BF02099964 ID - Klenk1986 ER - TY - JOUR AU - Pruesse, E. AU - Quast, C. AU - Knittel, K. AU - Fuchs, B. M. AU - Ludwig, W. AU - Peplies, J. AU - Glöckner, F. O. PY - 2007 DA - 2007// TI - SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm864 DO - 10.1093/nar/gkm864 ID - Pruesse2007 ER - TY - JOUR AU - MacKenzie, S. PY - 2001 DA - 2001// TI - High-throughput interpretation of pathways and biology JO - Drug News Perspect VL - 14 ID - MacKenzie2001 ER - TY - JOUR AU - Konstantinidis, K. T. AU - Tiedje, J. M. PY - 2005 DA - 2005// TI - Genomic insights that advance the species definition for prokaryotes JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0409727102 DO - 10.1073/pnas.0409727102 ID - Konstantinidis2005 ER - TY - JOUR AU - Deloger, M. AU - Karoui, M. E. AU - Petit, M. A. PY - 2009 DA - 2009// TI - A genomic distance based on MUM indicates discontinuity between most bacterial species and genera JO - J Bacteriol VL - 191 UR - https://doi.org/10.1128/JB.01202-08 DO - 10.1128/JB.01202-08 ID - Deloger2009 ER - TY - JOUR AU - Goris, J. AU - Konstantinidis, K. T. AU - Klappenbach, J. A. AU - Coenye, T. AU - Vandamme, P. AU - Tiedje, J. M. PY - 2007 DA - 2007// TI - DNA-DNA hybridization values and their relationship to whole-genome sequence similarities JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.64483-0 DO - 10.1099/ijs.0.64483-0 ID - Goris2007 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT — the BLAST-like alignment tool JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229202. Article published online before March 2002 DO - 10.1101/gr.229202. Article published online before March 2002 ID - Kent2002 ER - TY - JOUR AU - Kurtz, S. AU - Phillippy, A. AU - Delcher, A. L. AU - Smoot, M. AU - Shumway, M. AU - Antonescu, C. AU - Salzberg, S. L. PY - 2004 DA - 2004// TI - Versatile and open software for comparing large genomes JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-2-r12 DO - 10.1186/gb-2004-5-2-r12 ID - Kurtz2004 ER - TY - JOUR AU - Auch, A. F. AU - Henz, S. R. AU - Holland, B. R. AU - Göker, M. PY - 2006 DA - 2006// TI - Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-350 DO - 10.1186/1471-2105-7-350 ID - Auch2006 ER - TY - CHAP AU - Charlebois, R. AU - Beiko, R. AU - Ragan, M. ED - Hirt, R. ED - Horner, D. PY - 2004 DA - 2004// TI - Genome phylogenies BT - Organelles, Genomes and Eukaryote Phylogeny PB - CRC Press CY - Boca Raton/London/New York/Washington, D.C. ID - Charlebois2004 ER - TY - JOUR AU - Clarke, G. D. P. AU - Beiko, R. G. AU - Ragan, M. A. AU - Charlebois, R. L. PY - 2002 DA - 2002// TI - Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores JO - J Bacteriol VL - 184 UR - https://doi.org/10.1128/JB.184.8.2072-2080.2002 DO - 10.1128/JB.184.8.2072-2080.2002 ID - Clarke2002 ER - TY - JOUR AU - Henz, S. R. AU - Huson, D. H. AU - Auch, A. F. AU - Nieselt-Struwe, K. AU - Schuster, S. C. PY - 2005 DA - 2005// TI - Whole-genome prokaryotic phylogeny JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bth324 DO - 10.1093/bioinformatics/bth324 ID - Henz2005 ER - TY - JOUR AU - Wolf, Y. I. AU - Rogozin, I. AU - Grishin, N. AU - Tatusov, R. AU - Koonin, E. PY - 2001 DA - 2001// TI - Genome trees constructed using five different approaches suggest new major bacterial clades JO - BMC Evol Biol VL - 1 UR - https://doi.org/10.1186/1471-2148-1-8 DO - 10.1186/1471-2148-1-8 ID - Wolf2001 ER - TY - JOUR AU - Stackebrandt, E. AU - Goebel, B. M. PY - 1994 DA - 1994// TI - Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in Bacteriology JO - Int J Syst Bacteriol VL - 44 UR - https://doi.org/10.1099/00207713-44-4-846 DO - 10.1099/00207713-44-4-846 ID - Stackebrandt1994 ER - TY - CHAP AU - Klenk, H. P. ED - Antranikian, G. PY - 2005 DA - 2005// TI - Genome der Prokaryonten BT - Angewandte Mikrobiologie PB - Springer Verlag CY - Berlin ID - Klenk2005 ER - TY - JOUR AU - Tettelin, H. AU - Feldblyum, T. PY - 2009 DA - 2009// TI - Bacterial genome sequencing JO - Methods Mol Biol VL - 551 UR - https://doi.org/10.1007/978-1-60327-999-4_18 DO - 10.1007/978-1-60327-999-4_18 ID - Tettelin2009 ER - TY - JOUR AU - Auch, A. F. AU - Klenk, H. P. AU - Göker, M. PY - 2010 DA - 2010// TI - Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs JO - Stand Genomic Sci VL - 2 ID - Auch2010 ER - TY - JOUR AU - Liolios, K. AU - Mavromatis, K. AU - Tavernarakis, N. AU - Kyrpides, N. C. PY - 2008 DA - 2008// TI - The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm884 DO - 10.1093/nar/gkm884 ID - Liolios2008 ER - TY - JOUR AU - Wu, D. AU - Hugenholtz, P. AU - Mavromatis, K. AU - Pukall, R. AU - Dalin, E. AU - Ivanova, N. N. AU - Kunin, V. AU - Goodwin, L. AU - Wu, M. AU - Tindall, B. J. PY - 2009 DA - 2009// TI - A phylogeny-driven genomic encyclopedia of Bacteria and Archaea JO - Nature VL - 462 UR - https://doi.org/10.1038/nature08656 DO - 10.1038/nature08656 ID - Wu2009 ER - TY - STD TI - Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol (In press). PubMed ID - ref32 ER - TY - JOUR AU - Schwartz, S. AU - Kent, W. J. AU - Smit, A. AU - Zhang, Z. AU - Baertsch, R. AU - Hardison, R. C. AU - Haussler, D. AU - Miller, W. PY - 2003 DA - 2003// TI - Humanmouse alignments with BLASTZ JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.809403 DO - 10.1101/gr.809403 ID - Schwartz2003 ER - TY - STD TI - Delgado-Friedrichs O, Dezulian T, Huson DH. A meta-viewer for biomolecular data. GI Jahrestagung 2003: 375–380. Software freely available from http://www-ab.informatik.uni-tuebingen.de/software/cgviz UR - http://www-ab.informatik.uni-tuebingen.de/ ID - ref34 ER - TY - STD TI - Auch AF, Henz SR, Göker M. Phylogenies from whole genomes: Methodological update within a distance-based framework. German Conference on Bioinformatics, 2006. Available online, urn:nbn:de:bsz:21-opus-34178 ID - ref35 ER - TY - BOOK AU - Sokal, R. R. AU - Rohlf, J. F. PY - 1969 DA - 1969// TI - Biometry: The principles and practice of statistics in biological research PB - W.H. Freeman and Company CY - San Francisco ID - Sokal1969 ER - TY - BOOK AU - Legendre, P. AU - Legendre, L. PY - 1998 DA - 1998// TI - Numerical ecology PB - Elsevier Science BV CY - Amsterdam ID - Legendre1998 ER - TY - STD TI - R: The R Project for Statistical Computing. 2005 http://www.r-project.org/. UR - http://www.r-project.org/ ID - ref38 ER - TY - JOUR AU - Lee, C. AU - Grasso, C. AU - Sharlow, M. F. PY - 2002 DA - 2002// TI - Multiple sequence alignment using partial order graphs JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.3.452 DO - 10.1093/bioinformatics/18.3.452 ID - Lee2002 ER - TY - BOOK AU - Swofford, D. L. PY - 2002 DA - 2002// TI - PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) PB - Sinauer Associates CY - Sunderland, MA ID - Swofford2002 ER - TY - JOUR AU - Lander, E. S. AU - Waterman, M. S. PY - 1988 DA - 1988// TI - Genomic mapping by fingerprinting random clones: a mathematical analysis JO - Genomics VL - 2 UR - https://doi.org/10.1016/0888-7543(88)90007-9 DO - 10.1016/0888-7543(88)90007-9 ID - Lander1988 ER - TY - JOUR AU - Göker, M. AU - Grimm, G. W. PY - 2008 DA - 2008// TI - General functions to transform associate data to host data and their use in phylogenetic inference from sequences with intra-individual variability JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-86 DO - 10.1186/1471-2148-8-86 ID - Göker2008 ER - TY - JOUR AU - Labeda, D. P. PY - 1998 DA - 1998// TI - DNA relatedness among the Streptomyces fulvissimus and Streptomyces griseoviridis phenotypic cluster groups JO - Int J Syst Bacteriol VL - 48 UR - https://doi.org/10.1099/00207713-48-3-829 DO - 10.1099/00207713-48-3-829 ID - Labeda1998 ER - TY - JOUR AU - Copeland, A. AU - Spring, S. AU - Göker, M. AU - Schneider, S. AU - Lapidus, A. AU - Glavina Del Rio, T. AU - Tice, H. AU - Cheng, J. F. AU - Lucas, S. AU - Chen, F. PY - 2009 DA - 2009// TI - Complete genome sequence of Desulfomicrobium baculatum type strain (XT) JO - Stand Genomic Sci VL - 1 UR - https://doi.org/10.4056/sigs.13134 DO - 10.4056/sigs.13134 ID - Copeland2009 ER - TY - STD TI - Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, et al. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T). Stand Genomic Sci (In press). ID - ref45 ER -