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

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

by Marco Salemi,Anne-Mieke Vandamme

ePub The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny download
Author:
Marco Salemi,Anne-Mieke Vandamme
ISBN13:
978-0521803908
ISBN:
052180390X
Language:
Publisher:
Cambridge University Press; 1 edition (September 1, 2003)
Category:
Subcategory:
Science & Mathematics
ePub file:
1745 kb
Fb2 file:
1922 kb
Other formats:
docx lrf rtf lrf
Rating:
4.9
Votes:
471

The book is REALLY a practical approach to Phylogenetic Analysis. Perfect to help conducting a graduate level course, with practical exercises and chapters written by the authors of softwares and methods

The book is REALLY a practical approach to Phylogenetic Analysis. Every Chapter has a Theory and Practice section that makes this book outstanding. The practical aspect is very easy to follow and understand. It is well written with a good basic background to Molecular Evolution. I strongly RECOMMEND this text for any Evolutionary Biologist. Perfect to help conducting a graduate level course, with practical exercises and chapters written by the authors of softwares and methods.

The book has grown out of Drs. Vandamme’s and Salemi’s annual course in these methods at the Katholieke Universiteit in Leuven, Belgium, where they have produced an exceptional workshop for eight years that does for Europe what a similar outstanding and long-running workshop at Woods Hole did for the United States and Canada. But the latter has not created a book like this. The coverage is comprehensive.

The Phylogenetic Handbook book. Goodreads helps you keep track of books you want to read. The Phylogenetic Handbook is a broad introduction to the theory. Start by marking The Phylogenetic Handbook: A Practical Approach To Dna And Protein Phylogeny as Want to Read: Want to Read savin. ant to Read.

Data analysis is a tricky business for biologists, compared to the business of collecting data

Data analysis is a tricky business for biologists, compared to the business of collecting data. For example, in laboratory work there are usually gold standards that have been developed, and these can be written down as an explicit protocol for anyone and everyone to follow. Even if you do not understand the protocol, you can still follow its instructions, secure in the knowledge that if you are even half-competent, then the results should be reliable.

1. Basic concepts of molecular evolution Anne-Mieke Vandamme 2. Sequence databases Guy Bottu and Marc Va. .

1 1.

Mitochondria1 DNA (mtDNA) restriction analysis was used to assess phylogenetic patterns among 21 taxa of the subfamily Coregoninae.

Current studies in this direction are discussed  . Mitochondria1 DNA (mtDNA) restriction analysis was used to assess phylogenetic patterns among 21 taxa of the subfamily Coregoninae. The genus Prosopium formed a very distinct group differing by 10% (sequence divergence estimate) from other species.

The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis

The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis.

The Phylogenetic Handbook is a broad, hands on guide to theory and . The book is REALLY a practical approach to Phylogenetic Analysis.

The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. Anne-Mieke Vandamme is a Full Professor in the Medical Faculty at the Katholieke Universiteit, Belgium, working in the field of clinical and epidemiological virology.

The Phylogenetic Handbook is a broad introduction to the theory and practice of nucleotide and amino acid phylogenetic analysis. As an unique feature of this book, each chapter contains an extensive practical section, in which step-by-step exercises on real data sets introduce the most widely used phylogeny software including CLUSTAL, PHYLIP, PAUP*, DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML and BOOTSCANNING. The book provides a strong background in basic topics: the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution.
  • 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.