The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny

ISBN: 052180390X

Edited by Marco Salemi, Anne-Mieke Vandamme

The Phylogenetic Handbook is a broad introduction to the theory and practice of nucleotide and amino acid phylogenetic analysis. As a unique feature of this book, each chapter contains an extensive practical section, in which step-by-step exercises on real data sets introduce the reader to the most widely-used phylogeny software including CLUSTAL, PHYLIP, PAUP*, DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML, and BOOTSCANNING. Chapters 1-10 provide a strong background in basic topics such as the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution. Additional chapters briefly survey special topics in evolution, for example modelling evolution with networks, studying recombination, testing for positive selection, and methods in population genetics. The book will be an invaluable resource for advanced level undergraduate and graduate students, as well as for professionals working in the fields of molecular biology and evolution.

1. Basic concepts of molecular evolution Anne-Mieke Vandamme
2. Sequence databases Guy Bottu and Marc Van Ranst
3. Multiple alignment Des Higgins
4. Nucleotide substitution models Korbinian Strimmer, Arndt von Heseler and Marco Salemi
5. Phylogeny inference based on distance models Yves Van de Peer and Marco Salemi
6. Phylogeny inference based on maximum liklihood methods with TREE-PUZZLE Korbinian Strimmer and Arndt von Haeseler
7. Phylogeny inference based on parsimony and other methods with PAUP* David L. Swofford and Jack Sullivan
8. Phylogenetic analysis using protein sequences Fred Opperdoes
9. Substitution rate calibration with TREECON Yves van de Peer
10. Selecting models of evolution David Posada
11. Analysis of coding sequences Yoshiyuki Suzuki and Takashi Gojobori
12. Splits Tree: a network based tool for exploring evolutionary relationships in molecular data Vincent Moulton
13. Data exploration and tetrapod phylogeny using DAMBE Xuhua Xia and Zheng Xia
14. Detecting recombination in viral sequences Mika Salminen
15. LAMARC: estimating population genetic parameters from molecular data Mary K. Kuhner.

Hardcover: 430 pages; September 1, 2003; Cambridge University Press