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Title: Inferring Phylogenies by Joseph Felsenstein ISBN: 0-87893-177-5 Publisher: Sinauer Associates Pub. Date: 04 September, 2003 Format: Paperback Volumes: 1 List Price(USD): $61.95 |
Average Customer Rating: 4.5 (2 reviews)
Rating: 4
Summary: first print
Comment: The book I bought is first printing version. Lots of typo inside..... I should correct them myself.-:(
Rating: 5
Summary: The encyclopedia
Comment: 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. He seems to have chosen a variety of well-known and important algorithms for full description, and left the minor or complex ones for the references.
If you just want to use one of the common phylogeny programs, you came to the wrong place. This is about fundamental techniques for creating programs - there's almost nothing here for the user who just wants the results. Such users won't even learn much more about the results they do get. Developers and statisticians who need detailed analyses will probably find what they they want, and lots more.
The only problem with the book is that it reads like an encyclopedia. Lots of developers can get lots of good work done without this level of knowledge. It will take a truly devoted reader to plow though it, as well as a good foundation in algorithm development and in probability and stats. If you are dedicated to becoming an expert in the practice and problems of phylogenetic analysis, though, I doubt that any other book will give you a third of the knowledge or a tenth of the breadth.
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Title: Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists by Barry G. Hall ISBN: 0878933115 Publisher: Sinauer Associates Pub. Date: 01 March, 2001 List Price(USD): $29.95 |
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Title: The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny by Marco Salemi, Anne-Mieke Vandamme ISBN: 052180390X Publisher: Cambridge University Press Pub. Date: 01 September, 2003 List Price(USD): $75.00 |
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Title: Tangled Trees: Phylogeny, Cospeciation, and Coevolution by Roderic D. M. Page ISBN: 0226644677 Publisher: University of Chicago Press Pub. Date: 01 September, 2002 List Price(USD): $28.00 |
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Title: Molecular Evolution and Phylogenetics by Masatoshi Nei, Sudhir Kumar, S. Kumar ISBN: 0195135857 Publisher: Oxford University Press Pub. Date: 15 August, 2000 List Price(USD): $64.50 |
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Title: Phylogenetics (Oxford Lecture Series in Mathematics and Its Applications, 24) by Charles Semple, Mike Steel ISBN: 0198509421 Publisher: Oxford University Press Pub. Date: 01 March, 2003 List Price(USD): $90.00 |
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