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Ch. 1 Introduction 1
Ch. 2 NumPy and SciPy 13
Ch. 3 Image Manipulation 29
Ch. 4 The Akando and Dancer Modules 37
Ch. 5 Statistics 53
Ch. 6 Parsing DNA Data Files 71
Ch. 7 Sequence Alignment 89
Ch. 8 Dynamic Programming 101
Ch. 9 Tandem Repeats 119
Ch. 10 Hidden Markov Models 125
Ch. 11 Genetic Algorithms 139
Ch. 12 Multiple Sequence Alignment 157
Ch. 13 Gapped Alignments 179
Ch. 14 Trees 197
Ch. 15 Text Mining 227
Ch. 16 Measuring Complexity 241
Ch. 17 Clustering 255
Ch. 18 Self-Organizing Maps 275
Ch. 19 Principal Component Analysis 289
Ch. 20 Species Identification 309
Ch. 21 Fourier Transforms 319
Ch. 22 Correlations 333
Ch. 23 Numerical Sequence Alignment 345
Ch. 24 Gene Expression Array Files 365
Ch. 25 Spot Finding and Measurement 375
Ch. 26 Spreadsheet Arrays and Data Displays 389
Ch. 27 Applications with Expression Arrays 401
Index 413
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