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This text focuses on using algorithms and discrete mathematics to solve biological problems. It systematically describes biological applications, the corresponding mathematical/computational problems, and various algorithmic solutions. The author also discusses the practical use of many algorithmic methods and describes what algorithms should be used in different situations. Each chapter contains an overview of the biological problem, a precise definition of the computational problem, a description of various methods, practical issues and further research, references to further reading, and a set of knowledge-testing exercises. Instruction and data for practical exercises are provided on the authors website.