Phylogenetic trees made easy: a how-to manual

✍ Scribed by Hall, Barry G

• Publisher: Sinauer Associates
• Year: 2018
• Tongue: English
• Leaves: 369
• Edition: Fifth edition
• Category: Library

✦ Synopsis

Read me first! -- Tutorial : estimate a tree! -- Acquiring the sequences -- Aligning the sequences -- Major methods for estimating phylogenetic trees -- Neighbor joining trees -- Drawing phylogenetic trees -- Parsimony -- Maximum likelihood -- Bayesian inference of trees using BEAST -- Which method should you use? -- Working with various computer platforms -- Phylogenetic networks -- Minimum spanning trees -- Time trees -- Reconstructing ancestral sequences -- Detecting adaptive evolution -- Estimating phylogenetic trees from whole genome sequences -- Some final advice: learn to program.

✦ Table of Contents

Cover......Page 1
Front Matter......Page 2
Copyright Page......Page 5
Dedication......Page 7
Acknowledgments......Page 8
Table of Contents......Page 10
Chapter 1 Read Me First!......Page 18
Just What Is a Phylogenetic Tree?......Page 19
Estimating Phylogenetic Trees: The Basics......Page 21
Beyond the Basics......Page 22
About Appendix VI: F.A.Q.......Page 24
FigTree......Page 25
Acknowledging Computer Programs......Page 26
The......Page 27
Why Create Phylogenetic Trees?......Page 28
A word about screen shots......Page 29
Search for Sequences Related to Your Sequence......Page 30
Decide Which Related Sequences to Include on Your Tree......Page 35
Establishing homology......Page 36
To include or not to include, that is the question......Page 37
Download the Sequences......Page 39
Align the Sequences......Page 44
Make a Neighbor Joining Tree......Page 45
Summary......Page 49
Problems arising from the vast size of the sequence databases......Page 50
Hunting Homologs: What Sequences Can Be Included on a Single Tree?......Page 51
Becoming More Familiar with BLAST......Page 52
Using the Nucleotide BLAST Page......Page 53
Using BLAST to Search for Related Protein Sequences......Page 56
Problems adding coding sequences of protein homologs to the Alignment Explorer......Page 60
Add a sequence......Page 64
Other Ways to Find Sequences of Interest (Beware! The Risks Are High)......Page 65
Aligning Sequences with MUSCLE......Page 70
Trim excess sequence......Page 74
Eliminate duplicate sequences......Page 75
Codons: Pairwise amino acid identity......Page 77
Non-coding DNA sequences......Page 78
How MUSCLE works......Page 79
Adjusting parameters to increase alignment speed......Page 80
Aligning Sequences with ClustalW......Page 81
Aligning Sequences with GUIDANCE2......Page 82
Viewing the results......Page 84
Eliminate unreliable parts of the alignment......Page 85
Saving the GUIDANCE2 alignment......Page 87
Chapter 5 Major Methods for Estimating Phylogenetic Trees......Page 88
Distance versus Character-Based Methods......Page 91
Using MEGA7 to Estimate a Neighbor Joining Tree......Page 94
Determine the suitability of the data for a Neighbor Joining tree......Page 97
Estimate the tree......Page 98
Unrooted and Rooted Trees......Page 105
Estimating the Reliability of a Tree......Page 108
What about Protein Sequences?......Page 116
Changing the Appearance of a Tree......Page 118
The Options dialog......Page 121
Branch styles......Page 125
Fine-tuning the appearance of a tree......Page 126
Finding an outgroup......Page 129
Subtrees......Page 131
Saving a tree description......Page 135
Captions......Page 136
Chapter 8 Parsimony......Page 138
MP Search Methods......Page 140
Using SeaView for Parsimony......Page 142
Estimating a bootstrap tree in SeaView......Page 150
Using MEGA to draw the tree estimated by SeaView......Page 153
Chapter 9 Maximum Likelihood......Page 158
ML Analysis Using MEGA......Page 160
Test alternative models......Page 161
Estimating the Reliability of an ML Tree by Bootstrapping......Page 165
What about Protein Sequences?......Page 166
BEAST: An Overview......Page 168
Prepare the Input Alignment File......Page 169
Run BEAUti......Page 170
Running BEAST......Page 179
Run Tracer......Page 182
Burnin......Page 183
Run TreeAnnotator......Page 185
What about Protein Sequences?......Page 186
Visualizing the BEAST Tree......Page 187
The icons above the tree......Page 189
Criteria to Consider......Page 192
Time and convenience......Page 193
Results of the Major Methods......Page 195
Command-line Programs......Page 200
Navigating among folders on the Mac......Page 201
The Line Endings Issue......Page 205
Running the Utility Programs......Page 206
Why Trees Are Not Always Sufficient......Page 208
Unrooted and Rooted Phylogenetic Networks......Page 209
Estimating networks from alignments......Page 215
Rooting an unrooted network......Page 221
Estimating networks from trees......Page 222
Consensus networks......Page 223
Supernetworks......Page 227
Using Dendroscope to Estimate Rooted Networks from Rooted Trees......Page 228
Why Use Minimum Spanning Trees?......Page 232
What is a minimum spanning tree?......Page 233
Using MSTgold to Estimate MSTs......Page 234
The MSTgold input files......Page 235
Running MSTgold with the ebgC data......Page 236
The MSTgold output......Page 237
Bootstrapping MSTgold......Page 240
Exporting MSTs from Graphviz......Page 242
An Alternative Data Set to Illustrate Some Additional Features of MSTgold......Page 243
An Alternative to Graphviz: Hypercube......Page 246
Preparations to Estimate a Time Tree......Page 248
Estimating a Time Tree......Page 251
Viewing the Relative Time Tree......Page 255
An Absolute Time Tree......Page 257
Postscript......Page 261
Chapter 16 Reconstructing Ancestral Sequences......Page 262
Construct the phylogeny......Page 263
Examine the ancestral states at each site in the alignment......Page 264
Estimate the ancestral sequence......Page 267
Calculating the ancestral protein sequence and amino acid probabilities......Page 273
How Accurate Are the Estimated Ancestral Sequences?......Page 274
Chapter 17 Detecting Adaptive Evolution......Page 276
Detecting overall selection......Page 278
Detecting selection between pairs......Page 280
Finding the region of the gene that has been subject to positive selection......Page 281
Using codeml to Detect Adaptive Evolution......Page 283
Installation......Page 284
Run codeml......Page 286
Questions that underlie the models......Page 290
A closer look at ebgC_1.out......Page 292
Compiling PAML yourself and running codeml without......Page 295
Chapter 18 Estimating Phylogenetic Trees from Whole Genome Sequences......Page 298
kSNP: An Alternative to Genome Alignment......Page 299
kChooser......Page 301
FCK......Page 302
Using kSNP3......Page 303
The steps in estimating phylogenetic trees from WGS using kSNP3......Page 304
Chapter 19 Some Final Advice: Learn to Program......Page 314
The MEGA format......Page 316
The FASTA format......Page 317
The Nexus format......Page 318
The PHYLIP format......Page 321
FastaConvert, MEGA, and SeaView......Page 322
Mac OS X: TextWrangler......Page 324
Linux: Gedit......Page 325
Introduction and History......Page 328
Terminal and Command Prompt: The Apps for Accessing the Command-line Environment......Page 329
Entering Commands......Page 330
Navigating in Terminal......Page 331
The Magic Trick......Page 332
What Is in the CWD? The......Page 333
The -a option......Page 334
The permissions column......Page 335
Command in Command Prompt......Page 336
Copy a file......Page 337
Clear the screen......Page 338
Mac OS X / Linux......Page 340
Windows......Page 341
Running Command-line Programs......Page 346
Error checking......Page 347
Appendix V Additional Programs......Page 348
Appendix VI Frequently Asked Questions......Page 352
Literature Cited......Page 356
Index to Major Program Discussions......Page 358
Subject Index......Page 362

✦ Subjects

Phylogeny--Data processing;Phylogeny -- Data processing