Volume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic systematics. This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries.
Volume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic systematics. This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries.
1. The Need for Change: Embracing the Genome William B. Whitman 2. An Introduction to Phylogenetics and The Tree of Life1 Tom A. Williams and Sarah E. Heap 3. The All-Species Living Tree Project Pablo Yarza and Raul Munoz 4. 16S rRNA Gene-based Identification of Bacteria and Archaea using the EzTaxon Server Mincheol Kim and Jongsik Chun 5. Revolutionising Prokaryotic Systematics Through Next-Generation Sequencing Vartul Sangal, Leena Nieminen, Nicholas P. Tucker and Paul A. Hoskisson 6. Whole Genome Analyses: Average Nucleotide Identity David R. Arahal 7. Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways Simon R. Harris and Chinyere K. Okoro 8. Identification of Conserved Indels that are useful for Classification and Evolutionary Studies Radhey S. Gupta 9. Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees Olga K.Kamneva and Naomi L. Ward 10. Multi-locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation Alison J. Cody, Julia S. Bennett and Martin C.J. Maiden 11. Multilocus Sequence Analysis: Bringing Bacterial Systematics to the Next Level Xiaoying Rong and Ying Huang 12. Bacterial Typing and Identification by Genomic Analysis of 16s-23s rRNA Intergenic Spacer (ITS) Sequences Volker Gürtler, Gangavarapu Subrahmanyam, Malathi Shakar, Biswajit Maiti and Indrani Karunasagar 13. MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria Peter Schumann and Thomas Maier 14. Continuing Importance of the "Phenotype? in the Genomic Era Peter Kämpfer
1. The Need for Change: Embracing the Genome William B. Whitman 2. An Introduction to Phylogenetics and The Tree of Life1 Tom A. Williams and Sarah E. Heap 3. The All-Species Living Tree Project Pablo Yarza and Raul Munoz 4. 16S rRNA Gene-based Identification of Bacteria and Archaea using the EzTaxon Server Mincheol Kim and Jongsik Chun 5. Revolutionising Prokaryotic Systematics Through Next-Generation Sequencing Vartul Sangal, Leena Nieminen, Nicholas P. Tucker and Paul A. Hoskisson 6. Whole Genome Analyses: Average Nucleotide Identity David R. Arahal 7. Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways Simon R. Harris and Chinyere K. Okoro 8. Identification of Conserved Indels that are useful for Classification and Evolutionary Studies Radhey S. Gupta 9. Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees Olga K.Kamneva and Naomi L. Ward 10. Multi-locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation Alison J. Cody, Julia S. Bennett and Martin C.J. Maiden 11. Multilocus Sequence Analysis: Bringing Bacterial Systematics to the Next Level Xiaoying Rong and Ying Huang 12. Bacterial Typing and Identification by Genomic Analysis of 16s-23s rRNA Intergenic Spacer (ITS) Sequences Volker Gürtler, Gangavarapu Subrahmanyam, Malathi Shakar, Biswajit Maiti and Indrani Karunasagar 13. MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria Peter Schumann and Thomas Maier 14. Continuing Importance of the "Phenotype? in the Genomic Era Peter Kämpfer
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