The Phylogenetic Handbook
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Home > Mathematics and Science Textbooks > Biology, life sciences > Life sciences: general issues > Genetics (non-medical) > The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny
The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny

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


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About the Book

The Phylogenetic Handbook is a broad introduction to the theory and practice of nucleotide and amino acid phylogenetic analysis. As an unique feature of this book, each chapter contains an extensive practical section, in which step-by-step exercises on real data sets introduce the most widely used phylogeny software including CLUSTAL, PHYLIP, PAUP , DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML and BOOTSCANNING. The book provides a strong background in basic topics: the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution.

Table of Contents:
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.

Review :
'… a good buy …'. Plant Systematics & Evolution 'Given the problems associated with traditional phylogenetic approaches in bacteria and many fungi, the book is a timely one, and a wide range of scientists will find much aid within. The book starts with an extremely well-written and rather welcome introduction to the basic concepts of molecular evolution … The text avoids getting bogged down in the minutiae of these approaches, a good indication of the concise and clear writing that the authors employ throughout. The impression is of an extremely well-edited guide. … this is a very useful introduction to the subject of phylogenetics, with chapters written by acknowledged experts in the field, and a well-thought out concept of practical sections for familiarisation with the main phylogenetic software packages. … We are sure that our copy will become increasingly well-thumbed as a reference source.' Bibliography of Systematic Mycology 'It is wide-ranging enough to be a worthwhile introduction to phylogenetic analysis, without getting lost in too much detail …'. Systematic Biology


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Product Details
  • ISBN-13: 9780521803908
  • Publisher: Cambridge University Press
  • Publisher Imprint: Cambridge University Press
  • Height: 256 mm
  • No of Pages: 430
  • Returnable: N
  • Returnable: N
  • Sub Title: A Practical Approach to DNA and Protein Phylogeny
  • Width: 182 mm
  • ISBN-10: 052180390X
  • Publisher Date: 27 Aug 2003
  • Binding: Hardback
  • Language: English
  • Returnable: N
  • Returnable: N
  • Spine Width: 30 mm
  • Weight: 1114 gr


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