Section 11 References

Andre, E., L. Goeminne, A. Cabibbe, P. Beckert, B. Kabamba Mukadi, V. Mathys, S. Gagneux, S. Niemann, J. Van Ingen, and E. Cambau. 2017. Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria.” Clinical Microbiology and Infection 23 (3): 167–72. https://doi.org/10.1016/j.cmi.2016.09.006.
Atkinson, Gemma C. 2015. The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life.” BMC Genomics 16 (1): 1–15. https://doi.org/10.1186/s12864-015-1289-7.
Campbell, Finlay, Camilla Strang, Neil Ferguson, Anne Cori, and Thibaut Jombart. 2018. When are pathogen genome sequences informative of transmission events? Edited by Colin Parrish. PLOS Pathogens 14 (2): e1006885. https://doi.org/10.1371/journal.ppat.1006885.
Cock, Peter J a, Christopher J Fields, Naohisa Goto, Michael L Heuer, and Peter M Rice. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 38 (6): 1767–71. https://doi.org/10.1093/nar/gkp1137.
Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.” Nature 393 (6685): 537–44. https://doi.org/10.1038/31159.
Dulai, Kanwaljit S., Miranda Von Dornum, John D. Mollon, and David M. Hunt. 1999. The evolution of trichromatic color vision by opsin gene duplication in new world and old world primates.” Genome Research 9 (7): 629–38. https://doi.org/10.1101/gr.9.7.629.
Graur, Dan, Yichen Zheng, Nicholas Price, Ricardo B R Azevedo, Rebecca A Zufall, and Eran Elhaik. 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution, February, 1–43. https://doi.org/10.1093/gbe/evt028.
Lesk, Arthur. 2017. Introduction to Genomics. 3rd ed. USA: Oxford University Press, Inc.
Lesk, Arthur M. 2019. Introduction to bioinformatics.
McLysaght, Aoife, Karsten Hokamp, and Kenneth H. Wolfe. 2002. Extensive genomic duplication during early chordate evolution.” Nature Genetics 31 (2): 200–204. https://doi.org/10.1038/ng884.
Philip, Noraini, Kenneth Francis Rodrigues, Timothy William, and Daisy Vanitha John. 2016. Whole genome sequencing of Mycobacterium tuberculosis SB24 isolated from Sabah, Malaysia.” Genomics Data 9: 137–39. https://doi.org/10.1016/j.gdata.2016.08.007.
Rambaut, Andrew, Edward C. Holmes, Áine O’Toole, Verity Hill, John T. McCrone, Christopher Ruis, Louis du Plessis, and Oliver G. Pybus. 2020. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.” Nature Microbiology. https://doi.org/10.1038/s41564-020-0770-5.
Rasmussen, Morten, Yingrui Li, Stinus Lindgreen, Jakob Skou Pedersen, Anders Albrechtsen, Ida Moltke, Mait Metspalu, et al. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463 (7282): 757–62. https://doi.org/10.1038/nature08835.
Rienhoff, Hugh Young. 2016. Reflections on my daughter’s DNA.” Applied & Translational Genomics 8 (March): 45–48. https://doi.org/10.1016/j.atg.2016.01.006.
Singh, Param Priya, and Hervé Isambert. 2020. OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates.” Nucleic Acids Research 48 (D1): D724–30. https://doi.org/10.1093/nar/gkz909.
Snyder, M. 2016. Genomics and Personalized Medicine: What Everyone Needs to Know. What Everyone Needs to Know. Oxford University Press. https://books.google.co.uk/books?id=Z85OCwAAQBAJ.
Thorvaldsdottir, H., James T Robinson, and Jill P Mesirov. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.” Briefings in Bioinformatics 14 (2): 178–92. https://doi.org/10.1093/bib/bbs017.