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1 | (10) |
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New and Improved Software |
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2 | (1) |
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Just What Is a Phylogenetic Tree? |
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3 | (1) |
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Estimating Phylogenetic Trees: The Basics |
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4 | (1) |
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5 | (1) |
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Learn More about the Principles |
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6 | (1) |
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About Appendix III F.A.Q. |
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7 | (1) |
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Computer Programs and Where to Obtain Them |
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7 | (2) |
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8 | (1) |
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8 | (1) |
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8 | (1) |
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8 | (1) |
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SplitsTree and Dendroscope |
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8 | (1) |
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8 | (1) |
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9 | (1) |
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Acknowledging Computer Programs |
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9 | (1) |
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The Phylogenetic Trees Made Easy Website |
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9 | (2) |
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Chapter 2 Tutorial: Estimate a Tree |
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11 | (18) |
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Why Create Phylogenetic Trees? |
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11 | (1) |
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12 | (1) |
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Macintosh and Linux users |
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12 | (1) |
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A word about screen shots |
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12 | (1) |
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Search for Sequences Related to Your Sequence |
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13 | (3) |
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Decide Which Related Sequences to Include on Your Tree |
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16 | (4) |
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17 | (1) |
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To include or not to include, that is the question |
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18 | (2) |
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20 | (3) |
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23 | (1) |
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Make a Neighbor Joining Tree |
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24 | (4) |
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28 | (1) |
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Chapter 3 Acquiring the Sequences |
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29 | (18) |
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Hunting Homologs: What Sequences Can Be Included on a Single Tree? |
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29 | (1) |
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Becoming More Familiar with BLAST |
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30 | (2) |
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32 | (1) |
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Using the Nucleotide BLAST Page |
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32 | (2) |
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Using BLAST to Search for Related Protein Sequences |
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34 | (4) |
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Finalizing Selected Sequences for a Tree |
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38 | (5) |
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Other Ways to Find Sequences of Interest (Beware! The Risks Are High) |
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43 | (4) |
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Chapter 4 Aligning the Sequences |
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47 | (14) |
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Aligning Sequences with MUSCLE |
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47 | (4) |
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Examine and Possibly Manually Adjust the Alignment |
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51 | (5) |
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51 | (3) |
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Eliminate duplicate sequences |
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54 | (2) |
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Check Average Identity to Estimate Reliability of the Alignment |
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56 | (2) |
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Codons: Pairwise amino acid identity |
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56 | (1) |
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57 | (1) |
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Increasing Alignment Speed by Adjusting MUSCLE's Parameter Settings |
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58 | (2) |
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58 | (1) |
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Adjusting parameters to increase alignment speed |
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59 | (1) |
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Aligning Sequences with Clusta/W |
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60 | (1) |
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Chapter 5 Major Methods for Estimating Phylogenetic Trees |
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61 | (8) |
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Learn More About Tree-Searching Methods |
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62 | (2) |
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Distance versus Character-Based Methods |
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64 | (1) |
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Learn More About Distance Methods |
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64 | (2) |
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Which Method Should You Use? |
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66 | (3) |
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66 | (1) |
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67 | (1) |
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67 | (2) |
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Chapter 6 Neighbor Joining Trees |
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69 | (22) |
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Using MEGA 5 to Estimate a Neighbor Joining Tree |
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69 | (1) |
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Learn More About Phylogenetic Trees |
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70 | (5) |
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Determine the suitability of the data for a Neighbor Joining tree |
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73 | (1) |
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74 | (1) |
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Learn More About Evolutionary Models |
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75 | (5) |
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Unrooted and Rooted trees |
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80 | (2) |
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Estimating the Reliability of a Tree |
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82 | (1) |
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Learn More About Estimating The Reliability Of Phylogenetic Trees |
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83 | (6) |
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What about Protein Sequences? |
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89 | (2) |
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Chapter 7 Drawing Phylogenetic Trees |
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91 | (20) |
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Changing the Appearance of a Tree |
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92 | (14) |
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94 | (2) |
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96 | (3) |
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Fine-tuning the appearance of a tree |
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99 | (3) |
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102 | (4) |
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106 | (2) |
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108 | (1) |
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108 | (1) |
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Saving a tree description |
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108 | (1) |
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108 | (1) |
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109 | (2) |
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111 | (12) |
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Learn More About Parsimony |
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111 | (2) |
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113 | (3) |
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Multiple Equally Parsimonious Trees |
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116 | (6) |
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Calculating branch lengths |
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117 | (1) |
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Consensus and bootstrap trees |
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118 | (4) |
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122 | (1) |
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Chapter 9 Maximum Likelihood |
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123 | (16) |
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Learn More About Maximum Likelihood |
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123 | (2) |
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125 | (9) |
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126 | (3) |
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129 | (3) |
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The special case of zero length branches |
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132 | (2) |
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Estimating the Reliability of an ML Tree by Bootstrapping |
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134 | (3) |
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What about Protein Sequences? |
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137 | (2) |
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Chapter 10 Bayesian Inference of Trees Using MrBayes |
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139 | (22) |
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139 | (2) |
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Learn More About Bayesian Inference |
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141 | (2) |
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Saving time (and perhaps your sanity) |
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142 | (1) |
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143 | (1) |
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A General Strategy for Estimating Trees Using MrBayes |
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143 | (1) |
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Creating the Execution File |
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144 | (4) |
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What the statements in the example mrbayes block do |
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145 | (3) |
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How the stoprule option of the mcmc command is implemented |
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148 | (1) |
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How Do You Run a MrBayes Analysis? |
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148 | (1) |
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More Complex (and More Useful) MrBayes Blocks |
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149 | (2) |
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149 | (1) |
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The nperts option of the mcmc command |
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150 | (1) |
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Coding sequences and the charset statement |
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150 | (1) |
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The Screen Output while MrBayes Is Running |
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151 | (1) |
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What If You Don't Get Convergence? |
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152 | (4) |
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What about Protein Sequences? |
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156 | (1) |
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Visualizing the MrBayes Tree |
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156 | (2) |
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158 | (3) |
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158 | (2) |
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160 | (1) |
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Chapter 11 Working with Various Computer Platforms |
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161 | (16) |
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161 | (1) |
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MEGA on the Macintosh Platform |
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162 | (3) |
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Navigating among folders on the Mac |
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162 | (3) |
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Printing trees and text from MEGA |
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165 | (1) |
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165 | (1) |
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Installing Command Line Programs |
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165 | (3) |
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Macintosh and Linux: Use the bin folder |
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166 | (1) |
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Windows: Create a bin folder and a path to it |
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166 | (2) |
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Command Line Programs: The Running Environment |
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168 | (4) |
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Windows: A brief visit to the Command Prompt program |
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168 | (2) |
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Macintosh and Linux: A brief visit to Terminal and Unix |
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170 | (2) |
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Acquiring and Installing MrBayes |
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172 | (2) |
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172 | (1) |
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Macintosh and Linux users |
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173 | (1) |
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Compile MrBayes for your Mac |
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173 | (1) |
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Running the Utility Programs |
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174 | (3) |
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Utility programs for Windows |
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175 | (1) |
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Utility programs for Macintosh and Linux |
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175 | (2) |
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Chapter 12 Advanced Alignment Using GUIDANCE |
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177 | (14) |
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Issues of Alignment Reliability |
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177 | (1) |
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177 | (1) |
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178 | (1) |
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178 | (1) |
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An Example Illustrated by the SmallData Data Set |
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179 | (11) |
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Make a file of the unaligned sequences in FASTA format |
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180 | (1) |
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180 | (2) |
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182 | (4) |
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Eliminate unreliable sequences |
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186 | (4) |
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190 | (1) |
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Chapter 13 Reconstructing Ancestral Sequences |
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191 | (12) |
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Using Mega to Estimate Ancestral Sequences by Maximum Likelihood |
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192 | (9) |
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192 | (1) |
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193 | (1) |
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Examine the ancestral states at each site in the alignment |
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194 | (2) |
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Estimate the ancestral sequence |
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196 | (5) |
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Calculating the ancestral protein sequence and amino acid probabilities |
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201 | (1) |
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How Accurate are the Estimated Ancestral Sequences? |
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201 | (2) |
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Chapter 14 Detecting Adaptive Evolution |
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203 | (16) |
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Effect of Alignment Accuracy on Detecting Adaptive Evolution |
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205 | (1) |
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Using Mega to Detect Adaptive Evolution |
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205 | (6) |
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Detecting overall selection |
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205 | (1) |
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Detecting selection between pairs |
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206 | (2) |
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Finding the region of the gene that has been subject to positive selection |
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208 | (3) |
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Using Codeml to Detect Adaptive Evolution |
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211 | (7) |
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211 | (1) |
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The files you need to run codeml |
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211 | (2) |
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Questions that underlie the models |
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213 | (1) |
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214 | (1) |
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Identify the branches along which selection may have occurred |
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214 | (2) |
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Test the statistical significance of the dN/dS ratios |
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216 | (2) |
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218 | (1) |
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Chapter 15 Phylogenetic Networks |
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219 | (30) |
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Why Trees Are Not Always Sufficient |
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219 | (2) |
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Unrooted and Rooted Phylogenetic Networks |
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221 | (1) |
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Using SplitsTree to Estimate Unrooted Phylogenetic Networks |
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221 | (2) |
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Estimating networks from alignments |
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221 | (2) |
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Learn More About Phylogenetic Networks |
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223 | (20) |
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Rooting an unrooted network |
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234 | (1) |
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Estimating networks from trees |
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235 | (1) |
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236 | (5) |
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241 | (2) |
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Using Dendroscope to Estimate Rooted Networks from Rooted Trees |
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243 | (6) |
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Chapter 16 Some Final Advice: Learn to Program |
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249 | (2) |
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Appendix I File Formats and Their Interconversion |
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251 | (8) |
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251 | (6) |
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251 | (1) |
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252 | (1) |
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253 | (3) |
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256 | (1) |
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257 | (2) |
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257 | (1) |
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Other format conversion programs |
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257 | (2) |
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Appendix II Additional Programs |
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259 | (4) |
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Appendix III Frequently Asked Questions |
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263 | (4) |
| Literature Cited |
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267 | (2) |
| Index to Major Program Discussions |
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269 | (6) |
| Subject Index |
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275 | |
