For example, the phylogenetics and sequence evolution is central to comparative genomics, trying to decipher the genome, and molecular epidemiology. This book presents the latest models, their biological relevance, their mathematical basis, their properties, and algorithms to infer them from data. A number of subfields of mathematics and computer science are involved: combinatorics, graph theory, stringology, probabilistic and Markov models, information theory, statistical inference, Monte Carlo methods, continuous and discrete Algorithmics. This book emerged from a meeting phylogenetic Mathematics & Evolution at the Mathematical Institute Henri Poincar Paris? in June 2005 and is based on country-balance-the-art reports presented by conference speakers.