Inferring Phylogenies

Rating:
Summary: More than what the title implies
Review: 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.

Rating:
Summary: very complete reference book
Review: 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.

Rating:
Summary: The encyclopedia
Review: 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.

Rating:
Summary: first print
Review: The book I bought is first printing version. Lots of typo inside..... I should correct them myself.-:(

Rating:
Summary: not well written
Review: This book, although apparently containing everything, is written in a very opaque style which makes it impossible to simply read through. It probably is a good reference to look in for particular topics, but it is not at all usable as an introduction.