Combinatorial aspects of genome rearrangements and haplotype networks

i Acknowledgements First and foremost I would like to thank my advisor Jean-Paul Doignon, without whom the present text would not lie before your eyes. Jean-Paul introduced me to the world of research and taught me a lot, from the day we started working on genome rearrangement problems, which were the subject of my Master's Thesis and which he also supervised. I would like to thank him for being a wonderful advisor and a wonderful professor (I could not possibly overemphasise his ability to explain even the most complex concepts in such a simple and interesting way), and for believing in me enough to supervise me as a Ph. D. student. Research is fun, especially when you reach results interesting enough to be published , but it also has its moments of loneliness, doubt and pain; I would like to thank Lin, my friends and my family for supporting me, helping me and bearing with me during those hard times, and reminding me that there is more to life than work. Colleagues from both Departments (Mathematics and Computer Science) have also been most helpful, both on a personal and on a professional level. I would like to take this opportunity to thank in particular Jean Cardinal, who has always been able to spare a few minutes for discussing problems and whose " algorithmic lunches " , as they are called, have been a nice and refreshing opportunity for informal discussions, presentation of results and exchange of ideas between enthusiastic people on various topics. I would especially like to thankÉric Tannier and Marie-France Sagot for inviting me to a one-week open problem session in Lyon in April 2006, as well as my other collaborators: Guillaume Fertin, Irena Rusu, and Stéphane Vialette, for believing in and eventually collaborating withÉric and I on a survey which would later become a book. I must creditÉric for that idea. I would also like to thank Jean-Stéphane Varré for inviting me to Lille in March 2008 and giving me the opportunity to present some of my work to the SEQUOIA bioinformatics team at INRIA. I am also grateful to the Fonds National de la Recherche Scientifique (F.N.R.S.) for supporting me with a F.R.I.A. (Fonds pour la formationà la Recherche dans l'Industrie et dans l'Agriculture) grant during those four years. Finally, I would like to thank you for the time you will spend on my dissertation, and …