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