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Inferring Phylogenies Paperback – September 4, 2003

ISBN-13: 978-0878931774 ISBN-10: 0878931775 Edition: 2nd

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Product Details

  • Paperback: 664 pages
  • Publisher: Sinauer Associates; 2 edition (September 4, 2003)
  • Language: English
  • ISBN-10: 0878931775
  • ISBN-13: 978-0878931774
  • Product Dimensions: 7 x 1.1 x 8.9 inches
  • Shipping Weight: 1.9 pounds (View shipping rates and policies)
  • Average Customer Review: 4.1 out of 5 stars  See all reviews (8 customer reviews)
  • Amazon Best Sellers Rank: #197,418 in Books (See Top 100 in Books)

Editorial Reviews

Review

"Felsenstein’s book … represents a truly majestic discussion of the inference and applications of phylogenetic trees." -- Edward C. Holmes, The Quarterly Review of Biology

"Occasionally a book is a classic by the time it is published, and this is it. … " -- David Penny, Systematic Biology

"The publication of Inferring Phylogenies is a milestone for evolutionary biology in general and phylogenetics in particular." --Fredrik Ronquist, Science

Joe Felsenstein has had more positive influence on the statistical revolution of phylogenetics than any other researcher in the field. For that reason, many biologists view him as the father of statistical phylogenetics. It was with this in mind that I finally got my hands on his long-awaited book, Inferring Phylogenies. The short answer is: it delivers. . . . Inferring Phylogenies is quite simply an instant classic. --AJ Drummond, Heredity

Occasionally a book is a classic by the time it is published, and this is it. . . . The breadth is very wide with all the main expected topics. . . . It is hard to imagine how any lab could function without this book. --David Penny, Systematic Biology

Joe Felsenstein has had more positive influence on the statistical revolution of phylogenetics than any other researcher in the field. For that reason, many biologists view him as the father of statistical phylogenetics. It was with this in mind that I finally got my hands on his long-awaited book, Inferring Phylogenies. The short answer is: it delivers. . . . Inferring Phylogenies is quite simply an instant classic. --AJ Drummond, Heredity

Occasionally a book is a classic by the time it is published, and this is it. . . . The breadth is very wide with all the main expected topics. . . . It is hard to imagine how any lab could function without this book. --David Penny, Systematic Biology

Joe Felsenstein has had more positive influence on the statistical revolution of phylogenetics than any other researcher in the field. For that reason, many biologists view him as the father of statistical phylogenetics. It was with this in mind that I finally got my hands on his long-awaited book, Inferring Phylogenies. The short answer is: it delivers. . . . Inferring Phylogenies is quite simply an instant classic. --AJ Drummond, Heredity

Occasionally a book is a classic by the time it is published, and this is it. . . . The breadth is very wide with all the main expected topics. . . . It is hard to imagine how any lab could function without this book. --David Penny, Systematic Biology

Joe Felsenstein has had more positive influence on the statistical revolution of phylogenetics than any other researcher in the field. For that reason, many biologists view him as the father of statistical phylogenetics. It was with this in mind that I finally got my hands on his long-awaited book, Inferring Phylogenies. The short answer is: it delivers. . . . Inferring Phylogenies is quite simply an instant classic. --AJ Drummond, Heredity

Occasionally a book is a classic by the time it is published, and this is it. . . . The breadth is very wide with all the main expected topics. . . . It is hard to imagine how any lab could function without this book. --David Penny, Systematic Biology

About the Author

JOSEPH FELSENSTEIN is Professor in the Department of Genome Sciences at the University of Washington.

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Customer Reviews

4.1 out of 5 stars
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Most Helpful Customer Reviews

46 of 50 people found the following review helpful By wiredweird HALL OF FAMETOP 500 REVIEWER on January 5, 2004
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It's fairly common to start with a few protein or DNA sequences from different species, and to try to figure out what the various lines of descent are that connect them. This book is about the computations that find the "family trees" based on molecular (or other) data.
The book is a goldmine. Among phylogeny programs, PHYLIP (supported since 1980) could well be the most popular - Felsenstein wrote it. In this, he covers an incredible number of techniques, drawn from dozens of fundamentally different insights into the problem of relatedness. Felsentein desribes many techniques, their variations, and their relationships to others. He describes every phase of the analysis, from interpreting raw data, through deducing trees and evaluating them statistically, to displaying them visually. Despite this book's thud factor - ove 600 pages - it can not cover every topic in full detail. That's when the book's references, about 50 pages of them, become valuable. Felsenstein welcomes the interested reader into every aspect of the field's literature.
Despite the huge body of theory and practice, there are still many disputes about the proper interpretations or approaches to some thorny issues. Felsenstein goes over the issues in some detail, and is not afraid to take sides when he sees reason to.
Felsenstein gives clear descriptions of many basic algorithms. There's no code here, but a diligent reader should be able to develop implementations of them. I could have hoped for better indexing of algorithms, but the chapter organization is clear enough to make any search brief. I could also have asked for more of the algorithms to be spelled out in implementable detail, but the book would have needed thousands of pages to include them all.
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19 of 20 people found the following review helpful By Roger Burks on May 29, 2006
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This new explanation of phylogenetic methods contains a good discussion of the merits and potential failings of many of the methods currently used to study phylogenetics. It may be very good for computer science students, who have a better grasp of the mathematics. It may also be good for biologists well versed in biostatistics, who want to know why systematists use certain, less easily handled, analytical methods. However, it is very difficult reading for other scientists who do not fully understand the complex math presented in the text. It also does not give a concinct summary of the assumptions and failings of each method. The bottom line is that this book is good for experts who easily understand algorithms, but not good for students who don't have a good handle on such things.
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28 of 32 people found the following review helpful By Jonathan Badger on July 5, 2004
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As one would expect, the majority of this book deals with the various algorithms for phylogenetic analysis (such as the various versions of parsimony, distance based methods, and likelihood methods), but the book covers more topics that this. In particular, the book covers methods of tree comparison such as the KHT and SH tests, which I found particularly welcome because the current literature covering these tests often are rather opaque to those who haven't followed it since their conception.
The only weak thing about about the book (besides the many typos, which should be fixed in the new printing anyway), is Felsenstein's rather acrimonious treatment of Bayesian methods, in which the Bayesian use of priors is criticized on philosophical grounds.
I was annoyed by this not because I'm a card-carrying Bayesian (which I'm certainly not), but rather because I would have thought that Felsenstein of all people, whose primary opponents in the 1980's were the members of the philosophically-minded Willi Hennig crowd (who always claimed that parsimony was "philosophically right" even when it gave the wrong answer), would realize the futility of arguing scientific issues on philosophical grounds. Bayesian methods, as all scientific methods, will win or lose based on how well they work in practice, despite turgid philosophizing on both sides of the issue.
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10 of 10 people found the following review helpful By Christine Petersen on January 16, 2005
Format: Paperback
Inferring phylogenies was much anticipated by the large audience which has used Felsenstein's programs, and his website which reviews and categorizes applied tree building and population genetics programs.

This book is very complete, and functions well as a reference book. It is not a book that would read from start to finish, and probably would not be the best text available for a general upper division course. We have used selected chapters for supplementary readings when appropriate in reading groups. However, due to its completeness, this would be one title that I would recommend that most people working with phylogenetics would require for their bookshelf.
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