EVOLVE reader 諸氏：
三中信宏（農環研）です．
下記は[8176]ですでにアナウンスした本です．
タイトルを見るだけでそそられる人も多いのでは？（笑）
何だかオンライン・ドキュメントを読んでいるような感じがする本です．（きっと確信犯だろーな） でも，リンク付きオンラインで利用した方がもっと便利ではなかったかとも思います．
※ 本書では不思議なことに MacClade が取り上げられていないんじゃないかな？
読者（ユーザー）のみなさん，この本についてのコメント歓迎です．
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【書名】Phylogenetic Trees Made Easy:
A How-to Manual for Molecular Biologists.
【著者】Barry G. Hall
【刊行】2001年03月
【出版】Sinauer Associates, Sunderland
【頁数】xii+179 pp.
【価格】US$ 24.95
【ISBN】0-87893-311-5 (paperback)
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【目次】
Acknowledgments
Table of contents
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Introduction: Read me first 1
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A brief overview
Learn more about the principles
Computer programs discussed and where to obtain them
Clustal X
PAUP*
MrBayes
Puzzle
CodonAlign
Programs that are not discussed but that might be useful
Download files and utilities from the web site
Some conventions used in this book
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Section 1 Tutorial: Create a tree! 7
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Why create phylogenetic trees?
Obtaning related sequences by BLAST search
Step 1
Step 2
Step 3
Downloading the selected sequences
Creating the multiple alignment
Creating the input file
Getting the data into Clustal X
Some general comments about creating alignments
Setting the alignment parameters
Creating the alignment
Refining and improving the alignment
Aligning new sequences to an existing alignment or
aligning two existing alignments
Phylogenetic analysis
Methods for constructing phylogenies
Using PAUP* to create a tree
Creating the input file
Creating a neighbor-joining tree with PAUP*
Exactly what is a phylogenetic tree?
Placing the root of a tree
Bootstrapping a tree
Saving and using tree files
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Section 2 Additional methods for creating trees 69
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Which method should be used?
Distance vs. character-based methods
Creating parsimony trees using PAUP*
Creating maximum likelihood DNA trees using PAUP*
Step 1: Set up the data file
Step 2: Create and run an execution file
Creating maximum likelihood protein trees using Puzzle
Using MrBayes to create Bayesian DNA trees
Creating the execution file
Getting help
What the statements in the example MrBayes block do
The mcmcp command
What about the other parameters under lset
Summarizing MrBayes
Sample blocks for MrBayes
Reliability of the consensus tree
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Section 3 Presenting and printing your trees 115
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To root or not to root?
Midpoint rooting
Rooting with an outgroup
Choosing what form of a tree to publish
Making a tree pretty: No just a cosmetic matter
Making an unruly phylogram pretty
Indicating branch lengths on trees
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Section 4 Fine-tuning alignments 133
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Section 5 Using MtBayes to reconstruct ancestral
DNA sequences 137
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Section 6 Dealing with some common ploblems 145
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DNA or protein phylogenies: Which is better?
Using CodonAlign for protein coding sequences
Running CodonAlign
The output file
Error messages
Use of the source code
The effects of including nonhomologous sequences
Using BLAST to assess the homology of two sequences
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Appendix 1 File formats and their interconversion using
PAUP* 153
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Formats used by programs discussed in this book
The FASTA format
The Clustal format
The Nexus format
Other file formats
Phylip 3.x
The GCG/MSF format
The NBRF/PIR format
Interconverting formats using PAUP*
Importing various file formats into PAUP*
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Appendix 2 Printing alignments 163
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Printing to assess the quality of an alignment
Printing alignments for publication
Literature cited 167
Index to major programs discussed 169
Subject index 173
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