Phylogenetic trees made easy : a how-to manual for molecular biologists / Barry G. Hall.

Format:

Book

Author/Creator:

Hall, Barry G., 1942-

Language:

English

Subjects (All):

Phylogeny--Data processing.

Phylogeny.

Molecular Biology--classification.

Medical Subjects:

Phylogeny.

Molecular Biology--classification.

Physical Description:

xii, 179 pages : illustrations ; 24 cm

Place of Publication:

Sunderland, Mass. : Sinauer, [2001]

Summary:

Erhard Scheibe is one of the most outstanding German philosophers of science. He has written extensively on all the problems that confront the philosophy of mathematics and physics: rationalism versus empiricism, the laws of nature, and reductionism. He has published books on the logical foundations of quantum mechanics and on the reduction of physical theories. Little of his work has been translated into English. This collection of 38 essays is intended to remedy this omission and to help to make Erhard Scheibe's philosophical ideas better known to an international audience.

Contents:

Introduction: Read Me First 1

Learn More About the Principles 2

Computer Programs Discussed and Where to Obtain Them 3

ClustalX 3

PAUP* 3

MrBayes 3

Puzzle 4

CodonAlign 4

Programs That Are Not Discussed but That Might Be Useful 4

Download Files and Utilities from the Web Site 5

Some Conventions Used in This Book 6

Section 1 Tutorial: Create a Tree! 7

Why Create Phylogenetic Trees? 7

Obtaining Related Sequences by a BLAST Search 8

Downloading the Selected Sequences 17

Creating the Multiple Alignment 19

Creating the Input File 20

Getting the Data into ClustalX 22

Some General Comments about Creating Alignments 23

Setting the Alignment Parameters 23

Creating the Alignment 28

Refining and Improving the Alignment 29

Aligning New Sequences to an Existing Alignment or Aligning Two Existing Alignments 34

Phylogenetic Analysis 37

Methods for Constructing Phylogenies 27

Using PAUP* to Create a Tree 37

Creating the Input File 38

Creating a Neighbor-Joining Tree with PAUP* 40

Exactly What Is a Phylogenetic Tree? 44

Learn More about Phylogenetic Trees 48

Placing the Root of a Tree 52

Learn More about Rooting Phylogenetic Trees 54

Bootstrapping a Tree 58

Learn More about Estimating the Reliability of Phylogenetic Trees 60

Saving and Using Tree Files 64

Section 2 Additional Methods for Creating Trees 69

Which Method Should You Use? 69

Learn More about Tree-Searching Methods 70

Distance vs. Character-Based Methods 73

Learn More about Distance Methods 74

Creating Parsimony Trees Using PAUP* 77

Learn More about Parsimony 78

Creating Maximum Likelihood DNA Trees Using PAUP* 86

Learn More about Maximum Likelihood 87

Step 1 Set Up the Data File 89

Step 2 Create and Run an Execution File 90

Learn More about Evolutionary Models 91

Creating Maximum Likelihood Protein Trees Using Puzzle 96

Using MrBayes to Create Bayesian DNA Trees 98

Creating the Execution File 99

Learn More about Bayesian Analysis 100

Getting Help 103

What the Statements in the Example MrBayes Block Do 106

The mcmcp Command 108

What About the Other Parameters Under lset? 109

Summarizing MrBayes 109

Sample Blocks for MrBayes 110

Reliability of the Consensus Tree 111

Section 3 Presenting and Printing Your Trees 115

To Root or Not to Root? 115

Midpoint Rooting 118

Rooting with an Outgroup 120

Choosing What Form of a Tree to Publish 126

Making a Tree Pretty: Not Just a Cosmetic Matter 126

Making an Unruly Phylogram Pretty 128

Indicating Branch Lengths on Trees 130

Section 4 Fine-Tuning Alignments 133

Section 5 Using MrBayes to Reconstruct Ancestral DNA Sequences 137

Section 6 Dealing with Some Common Problems 145

DNA or Protein Phylogenies: Which Is Better? 145

Using CodonAlign for Protein Coding Sequences 146

Running CodonAlign 147

The Output File 148

Error Messages 148

Use of the Source Code 148

The Effects of Including Nonhomologous Sequences 149

Using BLAST to Assess the Homology of Two Sequences 150

Appendix I File Formats and Their Interconversion Using PAUP* 153

Formats Used by Programs Discussed in this Book 153

The FASTA Format 153

The Clustal Format 154

The Nexus Format 155

Other File Formats 157

Phylip 3.x 157

The GCG/MSF format 159

The NBRF/PIR format 160

Interconverting Formats Using PAUP* 161

Importing Various File Formats into PAUP* 161

Appendix II Printing Alignments 163

Printing to assess the quality of an alignment 163

Printing alignments for publication 164.

Notes:

Includes bibliographical references (pages [167]-168) and indexes.

ISBN:

0878933115

OCLC:

45835566