The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing / Edition 2

The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing / Edition 2

by Philippe Lemey
     
 

A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.See more details below

Overview

A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

Product Details

ISBN-13:
9780521730716
Publisher:
Cambridge University Press
Publication date:
05/31/2009
Edition description:
New Edition
Pages:
750
Sales rank:
755,775
Product dimensions:
6.90(w) x 9.70(h) x 1.40(d)

Table of Contents

Part I. Introduction:
1. Basic concepts of molecular evolution Anne-Mieke Vandamme;
Part II. Data Preparation:
2. Sequence databases and database searching Guy Bottu, Marc Van Ranst and Philippe Lemey;
3. Multiple sequence alignment Des Higgins and Philippe Lemey;
Part III. Phylogenetic Inference:
4. Nucleotide substitution models Korbinian Strimmer, Arndt von Haeseler and Marco Salemi;
5. Phylogenetic inference based on distance methods Yves Van de Peer and Marco Salemi;
6. Phylogenetic inference using maximum likelihood methods Heiko A. Schmidt and Arndt von Haeseler;
7. Bayesian phylogenetic analysis using MRBAYES Fredrik Ronquist, Paul van der Mark and John P. Huelsenbeck;
8. Phylogeny inference based on parsimony and other methods using PAUP* David L. Swofford and Jack Sullivan;
9. Phylogenetic analysis using protein sequences Fred R. Opperdoes and Philippe Lemey;
Part IV. Testing Models and Trees:
10. Selecting models of evolution David Posada;
11. Molecular clock analysis Philippe Lemey and David Posada;
12. Testing tree topologies Heiko Schmidt;
Part V. Molecular Adaptation:
13. Natural selection and adaptation of molecular sequences Oliver G. Pybus and Beth Shapiro;
14. Estimating selection pressures on alignments of coding sequences Sergei L. Kosakovsky Pond, Art F. Y. Poon, and Simon D. W. Frost;
Part VI. Recombination:
15. Introduction to recombination detection Philippe Lemey and David Posada;
16. Detecting and characterizing individual recombination events Mika Salminen and Darren Martin;
Part VII. Population Genetics:
17. The coalescent: population genetic inference using genealogies Allen Rodrigo;
18. Bayesian evolutionary analysis by sampling trees Alexei Drummond and Andrew Rambaut;
19. LAMARC: estimating population genetic parameters from molecular data Mary K. Kuhner;
Part VIII. Additional Topics:
20. Assessing substitution saturation with DAMBE Xuhua Xia and Philippe Lemey;
21. Split networks: a tool for exploring complex evolutionary relationships in molecular data Vincent Moulton and Katharina T. Huber.

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