Introduction: Read Me First |
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1 | (1) |
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A Brief Overview of the Second Edition |
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2 | (1) |
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Time-Limited Copy of the PAUP*4.0 Program |
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3 | (1) |
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Learn More about the Principles |
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4 | (1) |
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Computer Programs Discussed and Where to Obtain Them |
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4 | (3) |
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5 | (1) |
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5 | (1) |
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5 | (1) |
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PHYLIP (PHYLogeny Inference Package) |
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6 | (1) |
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6 | (1) |
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7 | (1) |
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7 | (1) |
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7 | (1) |
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Files and Utilities on the ``Phylogenetics Made Easy'' Website and CD |
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7 | (1) |
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Some Conventions Used in This Book |
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8 | (1) |
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9 | (52) |
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Why Create Phylogenetic Trees? |
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9 | (1) |
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Obtaining Related Sequences by a BLAST Search |
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10 | (13) |
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Step 1: Go to the BLAST Website |
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11 | (2) |
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Step 2: Use BLAST to Search for Sequences Related to Your Sequence |
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13 | (1) |
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Step 3: Decide Which Related Sequences to Include on Your Tree |
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14 | (6) |
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Downloading the Selected Sequences |
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20 | (3) |
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Creating the Multiple Alignment |
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23 | (17) |
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24 | (2) |
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Getting the Data into ClustalX |
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26 | (1) |
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Some General Comments about Creating Alignments |
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27 | (1) |
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Setting the Alignment Parameters |
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27 | (5) |
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32 | (1) |
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Refining and Improving the Alignment |
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33 | (5) |
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Aligning New Sequences to an Existing Alignment, or Aligning Two Existing Alignments |
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38 | (2) |
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40 | (2) |
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Exactly What Is a Phylogenetic Tree? |
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41 | (1) |
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Methods for Constructing Phylogenies |
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41 | (1) |
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Learn More About Phylogenetic Trees |
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42 | (10) |
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Using ClustalX to Create a Neighbor Joining Tree |
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46 | (1) |
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Drawing the Tree Using Tree View |
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47 | (1) |
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Tree Formats: Different Appearances of the Same Tree |
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47 | (3) |
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50 | (2) |
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Learn More About Estimating The Reliability of Phylogenetic Trees |
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52 | (4) |
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Placing the Root of a Tree |
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53 | (3) |
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Learng More About Rooting Phylogenetic Trees |
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56 | (4) |
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Printing and Saving the Tree |
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59 | (1) |
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60 | (1) |
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Basic Elements in Creating and Presenting Trees |
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61 | (96) |
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Selecting Homologs: What Sequences Can Be Put on a Single Tree? |
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61 | (3) |
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64 | (4) |
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Major Methods for Creating Trees |
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68 | (2) |
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Which Method Should You Use? |
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68 | (1) |
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Distance versus Character-Based Methods |
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69 | (1) |
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Learn More About Tree-Searching Methods |
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70 | (4) |
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Learn More About Distance Methods |
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74 | (2) |
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Data Files Used to Illustrate Methods |
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76 | (1) |
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Using PAUP* to Create Trees |
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76 | (18) |
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77 | (3) |
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Creating Neighbor-Joining Trees Using PAUP* |
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80 | (12) |
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Creating Parsimony Trees Using PAUP* |
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92 | (2) |
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Learn More About Parsimony |
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94 | (10) |
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Creating a Consensus Tree Using PAUP* |
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100 | (2) |
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Creating Maximum Likelihood DNA Trees Using PAUP* |
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102 | (2) |
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Learn More About Maximum Likelihood |
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104 | (6) |
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Learn More About Evolutionary Methods |
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110 | (4) |
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Creating Maximum-Likelihood Protein Trees Using Tree-Puzzle |
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114 | (4) |
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Creating Bayesian Trees Using MrBayes |
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118 | (2) |
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Creating the Execution File |
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119 | (1) |
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Learn More About Bayesian Analysis |
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120 | (15) |
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What the Statements in the Example MrBayes Block Do |
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123 | (5) |
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Interpreting MrBayes Results |
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128 | (2) |
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Sample Blocks for MrBayes |
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130 | (2) |
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132 | (3) |
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Presenting and Printing Your Trees |
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135 | (12) |
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Opening Tree Files in PAUP* |
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135 | (4) |
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139 | (8) |
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Choosing What Form of a Tree to Publish |
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147 | (1) |
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Making a Tree Pretty: Not Just a Cosmetic Matter |
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148 | (4) |
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DNA Phylogeny or Protein Phylogeny: Which Is Better? |
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152 | (5) |
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154 | (3) |
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Advanced Elements in Constructing Trees |
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157 | (22) |
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Reconstructing Ancestral DNA Sequences |
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157 | (10) |
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Ancestral Sequences for Parsimony and Maximum Likelihood Trees Using PAUP* |
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158 | (3) |
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Ancestral Sequences for Parsimony using PHYLIP |
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161 | (6) |
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Using Protein Structure Information to Construct Very Deep Phylogenies |
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167 | (6) |
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Analyzing Trees for Evidence of Adaptive Evolution by Detecting Positive Selection in a Phylogeny |
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173 | (6) |
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Using Alternative Software to Construct and Present Trees |
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179 | (14) |
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Using PAUP* with Windows or Unix |
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179 | (8) |
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Opening and Viewing Files |
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180 | (2) |
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182 | (3) |
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185 | (2) |
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187 | (6) |
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General Features of PHYLIP Programs |
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188 | (1) |
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189 | (1) |
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190 | (1) |
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190 | (1) |
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191 | (1) |
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191 | (2) |
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Appendix I File Formats and Their Interconversion |
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193 | (12) |
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Formats Used by Programs Discussed in this Book |
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193 | (6) |
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193 | (1) |
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194 | (1) |
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195 | (2) |
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197 | (2) |
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199 | (2) |
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The GCG/MSF Format and PileUp |
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199 | (1) |
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200 | (1) |
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Interconverting Formats Using PAUP* |
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201 | (2) |
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Importing Various File Formats into PAUP* |
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201 | (1) |
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Exporting Various File Formats from PAUP* |
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202 | (1) |
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Interconverting Interleaved and Sequential Formatted PHYLIP Files |
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203 | (2) |
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Appendix II Printing Alignments |
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205 | (2) |
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Printing to Assess the Quality of the Alignment |
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205 | (1) |
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Printing Alignments for Publication |
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206 | (1) |
Literature Cited |
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207 | (2) |
Index to Major Programs Discussed |
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209 | (6) |
Subject Index |
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215 | |