Stationarity and reversibility in the nucleotide evolutionary process [Elektronische Ressource] / Federico Squartini

Stationarity and Reversibility in theNucleotide Evolutionary ProcessFederico SquartiniDissertation zur Erlangung des Gradeseines Doktors der Naturwissenschaften (Dr. rer. nat.)am Fachbereich Mathematik und Informatikder Freien Universitat BerlinGutachter:Prof. Dr. Martin VingronProf. Dr. Arndt von Haeseler1. Referent: Prof. Dr. Martin Vingron2. Prof. Dr. Arndt Von HaeselerTag der Promotion: 3.Mai 2010AcknowledgmentsAll the research contained in this work was carried out at the Max Planck Institutefor Molecular Genetics in Berlin, department of Computational Molecular Biology. Theyears spent in the institute have been an enriching experience, which has greatly helpedme bringing my scienti c skills to maturity.I specially thank Peter Arndt for choosing me as his PhD student and supervising myresearch, Martin Vingron for giving me the opportunity to work in his department, andHannes Luz for all the invaluable help he has given me during my years in Berlin.Many thanks also go to my friends and colleagues in the Max Planck Institute, too manyto mention here, for the interesting discussions and the enduring encouragement.Finally, I thank my parents, who never failed to support me during my studies.Federico Squartini Berlin, May 2010iiiContentsPreface i1 Introduction 11.1 DNA, the molecule of life . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.2 The central dogma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.