Phylogenetic Trees Made Easy: A How-To Manual (5th Edition)

Cover
Front Matter
Copyright Page
Dedication
Acknowledgments
Table of Contents
Chapter 1 Read Me First!
New and Improved Software
Just What Is a Phylogenetic Tree?
Estimating Phylogenetic Trees: The Basics
Beyond the Basics
Learn More about the Principles
About Appendix VI: F.A.Q.
Computer Programs and Where to Obtain Them
MEGA7
BEAST
FigTree
codeml
SplitsTree and Dendroscope
Graphviz
Utility Programs
Text Editors
Acknowledging Computer Programs
Website
The
Chapter 2 Tutorial: Estimate a Tree
Why Create Phylogenetic Trees?
About this Tutorial
Macintosh and Linux users
A word about screen shots
Search for Sequences Related to Your Sequence
Decide Which Related Sequences to Include on Your Tree
Establishing homology
To include or not to include, that is the question
Download the Sequences
Align the Sequences
Make a Neighbor Joining Tree
Summary
Chapter 3 Acquiring the Sequences
Background
Problems arising from the vast size of the sequence databases
The query sequences
Hunting Homologs: What Sequences Can Be Included on a Single Tree?
Becoming More Familiar with BLAST
BLAST help
Using the Nucleotide BLAST Page
Using BLAST to Search for Related Protein Sequences
Finalizing Selected Sequences for a Tree
Problems adding coding sequences of protein homologs to the Alignment Explorer
Adding Sequences to and Removing Sequences from the Alignment Explorer
Add a sequence
Import a file of sequences
Delete a sequence
Other Ways to Find Sequences of Interest (Beware! The Risks Are High)
Chapter 4 Aligning the Sequences
Aligning Sequences with MUSCLE
Examine and Possibly Manually Adjust the Alignment
Trim excess sequence
Eliminate duplicate sequences
Check Average Identity to Estimate Reliability of the Alignment
Codons: Pairwise amino acid identity
Non-coding DNA sequences
Increasing Alignment Speed by Adjusting MUSCLE’s Parameter Settings
How MUSCLE works
Adjusting parameters to increase alignment speed
Aligning Sequences with ClustalW
Aligning Sequences with GUIDANCE2
Viewing the results
Eliminate unreliable parts of the alignment
Saving the GUIDANCE2 alignment
Chapter 5 Major Methods for Estimating Phylogenetic Trees
Distance versus Character-Based Methods
Chapter 6 Neighbor Joining Trees
Using MEGA7 to Estimate a Neighbor Joining Tree
Determine the suitability of the data for a Neighbor Joining tree
Estimate the tree
Unrooted and Rooted Trees
Estimating the Reliability of a Tree
What about Protein Sequences?
Chapter 7 Drawing Phylogenetic Trees
Changing the Appearance of a Tree
The Options dialog
Branch styles
Fine-tuning the appearance of a tree
Rooting a Tree
Finding an outgroup
Subtrees
Saving Trees
Saving a tree description
Saving a tree image
Captions
Chapter 8 Parsimony
MP Search Methods
Using SeaView for Parsimony
Estimating a bootstrap tree in SeaView
Using MEGA to draw the tree estimated by SeaView
Chapter 9 Maximum Likelihood
ML Analysis Using MEGA
Test alternative models
Estimating the Reliability of an ML Tree by Bootstrapping
What about Protein Sequences?
Chapter 10 Bayesian Inference of Trees Using BEAST
BEAST: An Overview
Installing BEAST
Prepare the Input Alignment File
Run BEAUti
Running BEAST
Run Tracer
Burnin
Run TreeAnnotator
What about Protein Sequences?
Visualizing the BEAST Tree
The icons above the tree
Chapter 11 Which Method Should You Use?
Criteria to Consider
Accuracy
Ease of interpretation
Time and convenience
Results of the Major Methods
Chapter 12 Working with Various Computer Platforms
Command-line Programs
MEGA on the Macintosh Platform
Navigating among folders on the Mac
Printing trees and text from MEGA
The Line Endings Issue
Running the Utility Programs
Chapter 13 Phylogenetic Networks
Why Trees Are Not Always Sufficient
Unrooted and Rooted Phylogenetic Networks
Using SplitsTree to Estimate Unrooted Phylogenetic Networks
Estimating networks from alignments
Rooting an unrooted network
Estimating networks from trees
Consensus networks
Supernetworks
Using Dendroscope to Estimate Rooted Networks from Rooted Trees
Chapter 14 Minimum Spanning Trees
Phylogenetic Trees!
Minimum Spanning Trees Are
Why Use Minimum Spanning Trees?
Origin of MSTs and the Issue of Reliability
What is a minimum spanning tree?
Using MSTgold to Estimate MSTs
The MSTgold input files
Two ways for MSTgold to calculate the initial distance matrix
Running MSTgold with the ebgC data
The MSTgold output
Bootstrapping MSTgold
Exporting MSTs from Graphviz
An Alternative Data Set to Illustrate Some Additional Features of MSTgold
An Alternative to Graphviz: Hypercube
Chapter 15 Time Trees
Preparations to Estimate a Time Tree
Estimating a Time Tree
Viewing the Relative Time Tree
An Absolute Time Tree
Effect of more calibration points on absolute time trees
Postscript
Chapter 16 Reconstructing Ancestral Sequences
Using MEGA to Estimate Ancestral Sequences by Maximum Likelihood
Create the alignment
Construct the phylogeny
Examine the ancestral states at each site in the alignment
Estimate the ancestral sequence
Calculating the ancestral protein sequence and amino acid probabilities
How Accurate Are the Estimated Ancestral Sequences?
Chapter 17 Detecting Adaptive Evolution
Effect of Alignment Accuracy on Detecting Adaptive Evolution
Using MEGA to Detect Adaptive Evolution
is an interesting example for considering adaptive evolution
Why
Detecting overall selection
Detecting selection between pairs
Finding the region of the gene that has been subject to positive selection
Using codeml to Detect Adaptive Evolution
Installation
Run codeml
Questions that underlie the models
A closer look at ebgC_1.out
Summary
Postscript
Compiling PAML yourself and running codeml without
Chapter 18 Estimating Phylogenetic Trees from Whole Genome Sequences
The Pan-Genome Problem
kSNP: An Alternative to Genome Alignment
kSNP 2.0
kChooser
FCK
Tree accuracy
Always run kChooser before running kSNP
Using kSNP3
The steps in estimating phylogenetic trees from WGS using kSNP3
Chapter 19 Some Final Advice: Learn to Program
Appendix I File Formats and Their Interconversion
Format Descriptions
The MEGA format
The FASTA format
The Nexus format
The PHYLIP format
Interconverting Formats
FastaConvert, MEGA, and SeaView
Appendix II Text Editors
Mac OS X: TextWrangler
Windows: Notepad++
Linux: Gedit
Appendix III The Command-line Environment
Introduction and History
Terminal and Command Prompt: The Apps for Accessing the Command-line Environment
The current directory
Entering Commands
Navigating in Terminal
The Magic Trick
Command (
What Is in the CWD? The
The -l option
The -a option
The permissions column
The
Command in Command Prompt
Some Other Important Commands
Copy a file
Move a file
Rename a file
Make a directory
Remove a directory
Remove a file
Print the contents of a file to the screen
Clear the screen
Appendix IV Installing and Running Command-line Programs
Installing Command-line Programs
Mac OS X / Linux
Windows
Running Command-line Programs
An example
The line endings issue
The example command line
Error checking
Appendix V Additional Programs
Appendix VI Frequently Asked Questions
Literature Cited
Index to Major Program Discussions
Subject Index