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This self-contained textbook covers fundamental aspects of sequence analysis with special emphasis on evolutionary biology, including sequence alignment, exact matching, phylogeny reconstruction, and coalescent simulation. It addresses these topics through a series of over 800 computer problems, ranging from elementary to research level, to enable learning by doing. Students solve the problems in the same computational environment used for decades in science – the Unix command line. This is available on all four major operating systems for PCs: Windows, macOS, chromeOS, and Linux. To learn...