Marco Salemi and Anne-Mieke Vandamme (eds.)
（2003年9月刊行，Cambridge University Press, Cambridge, xxiv+406 pp., ISBN:052180390X [hbk] → 版元ページ）
よくも悪くも「分子系統学ハンドブック」．改訂版が2009年に出ているのに，初版がまだ購入可能というのはフシギなことではある．
【目次】
Foreword xvii
Acknowledgments xxi
Contributors xxiii
1. Basic concepts of molecular evolution / Anne-Mieke Vandamme 1
2. Sequence databases / Guy Bottu and Marc Van Ranst 24
3. Multiple alignment / Des Higgins 45
4. Nucleotide substitution models / Korbinian Strimmer and Arndt von Haeseler 72
5. Phylogeny inference based on distance models / Yves Van de Peer 101
6. Phylogeny inference based on maximum liklihood methods with TREE-PUZZLE / Arndt von Haeseler and Korbinian Strimmer 137
7. Phylogeny inference based on parsimony and other methods with PAUP* / David L. Swofford and Jack Sullivan 160
8. Phylogenetic analysis using protein sequences / Fred R. Opperdoes 207
9. Substitution rate calibration with TREECON / Yves van de Peer 236
10. Selecting models of evolution / David Posada 256
11. Analysis of coding sequences / Yoshiyuki Suzuki and Takashi Gojobori 283
12. Splits Tree: a network based tool for exploring evolutionary relationships in molecular data / Vincent Moulton 312
13. Data exploration and tetrapod phylogeny using DAMBE / Xuhua Xia and Zheng Xie 329
14. Detecting recombination in viral sequences / Mika Salminen 348
15. LAMARC: estimating population genetic parameters from molecular data / Mary K. Kuhner 378
Index 399
