| Preface | p. xi |
| Introduction | p. 1 |
| Original problems | p. 2 |
| Additional problems | p. 5 |
| Further reading | p. 23 |
| Pairwise alignment | p. 24 |
| Original problems | p. 24 |
| Additional problems and theory | p. 43 |
| Derivation of the amino acid substitution matrices (PAM series) | p. 46 |
| Distributions of similarity scores | p. 57 |
| Distribution of the length of the longest common word among several unrelated sequences | p. 62 |
| Further reading | p. 65 |
| Markov chains and hidden Markov models | p. 67 |
| Original problems | p. 68 |
| Additional problems and theory | p. 77 |
| Probabilistic models for sequences of symbols: selection of the model and parameter estimation | p. 86 |
| Bayesian approach to sequence composition analysis: the segmentation model by Liu and Lawrence | p. 95 |
| Further reading | p. 102 |
| Pairwise alignment using HMMs | p. 104 |
| Original problems | p. 105 |
| Additional problems | p. 113 |
| Further reading | p. 125 |
| Profile HMMs for sequence families | p. 126 |
| Original problems | p. 127 |
| Additional problems and theory | p. 137 |
| Discrimination function and maximum discrimination weights | p. 150 |
| Further reading | p. 161 |
| Multiple sequence alignment methods | p. 162 |
| Original problem | p. 163 |
| Additional problems and theory | p. 163 |
| Carrillo-Lipman multiple alignment algorithm | p. 164 |
| Progressive alignments: the Feng-Doolittle algorithm | p. 171 |
| Gibbs sampling algorithm for local multiple alignment | p. 179 |
| Further reading | p. 181 |
| Building phylogenetic trees | p. 183 |
| Original problems | p. 183 |
| Additional problems | p. 211 |
| Further reading | p. 215 |
| Probabilistic approaches to phylogeny | p. 218 |
| Original problems | p. 219 |
| Bayesian approach to finding the optimal tree and the Mau-Newton-Larget algorithm | p. 235 |
| Additional problems and theory | p. 259 |
| Relationship between sequence evolution models described by the Markov and the Poisson processes | p. 264 |
| Thorne-Kishino-Felsenstein model of sequence evolution with substitutions, insertions, and deletions | p. 270 |
| More on the rates of substitution | p. 275 |
| Further reading | p. 277 |
| Transformational grammars | p. 279 |
| Original problems | p. 280 |
| Further reading | p. 290 |
| RNA structure analysis | p. 291 |
| Original problems | p. 292 |
| Further reading | p. 308 |
| Background on probability | p. 311 |
| Original problems | p. 311 |
| Additional problem | p. 326 |
| Further reading | p. 327 |
| References | p. 328 |
| Index | p. 343 |
| Table of Contents provided by Ingram. All Rights Reserved. |