Customer Reviews

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

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I came across this book while doing some phylogenetic analysis and found it very useful.

The first two chapters give some background information on molecular evolution and sequence databases, as well as a downloadable dataset used throughout the book.

The real business starts from chapter 3--multiple sequence alignment (MSA). Problems and algorithms of MSA are briefly reviewed. Here you know how CLUSTALW and T-Coffee work. The presentation of the progressive alignment used in CLUSTALW is especially clear. However, other popular programs are not metioned, probably they are not available or not widely used at the time when the book was written. I recommend PROCONS and MUSCLE for protein alignment and DIALIGN-T for both dna and protein alignment. Check them out.

Chapter 4 reviews nucleotide substitution model, concise and not much math on continuous-time Markov chain(CTMC). A chart shows the relationship between popular models including GTR, TN93, HKY85, F84, F81, K80 and JC. I like it. To know more details of CTMC of these models, however, you need to consult other books. Exercises using PHYLIP and DAMBE can be found.

One someone have the sequence aligned, and genetic/evolutionary distance between them adjusted using say JC, she/he is ready to jump to the next chapter 5 -- Phylogeny Inferrence based on distance methods. Here the outdated UPGMA, mainstream NJ and Fitch-Morgoliash methods are presented by examples, effectively cleaning the fog before these ACRONYM. Bootstrapping and Jacknifing, the two methods for assessing quality of phylogeny, are briefly explained, then progress to exercise using PHYLIP.

The next two chapters are maximum-likelihood with TREE-PUZZLE, and Parimony* (* means MP+ML+Distance) in PAUP*.

Working on dna or protein sequences sometimes can mean a whole lot of difference, these topics are dealt in chapter 8--Phylogenetic analysis using protein sequences and chapter 9--analysis of nucleotide sequences using TREECON.

If you only need to get the tree, you can stop here. The remainign chapters either deal with dN/dS, detecting recomination, or centered on particular software packages including SplitsTree,LAMARC and DAMBE(A heavily used package in this book another is PHYLIP).

Overall, the book is comprehensive, well balanced between practice and theory. Though contributed by different authors, the two editors seamlessly wave these chapters into a nice book. Bravo to them!

My only concern is book does not cover many widely-used programs, but we, the arduous tree constructors, can find them out by ourselves, do we?

it is very convenient and handy for a junior student.