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Phylogenetic Trees Made Easy: A How-To Manual 5th Revised edition [Pehme köide]

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  • Formaat: Paperback / softback, 372 pages, kõrgus x laius x paksus: 175x231x15 mm, kaal: 739 g, 310 p., 1 Paperback / softback
  • Ilmumisaeg: 01-Oct-2017
  • Kirjastus: Oxford University Press Inc
  • ISBN-10: 1605357103
  • ISBN-13: 9781605357102
Teised raamatud teemal:
Phylogenetic Trees Made Easy: A How-To Manual 5th Revised editionSuurem pilt
  • Formaat: Paperback / softback, 372 pages, kõrgus x laius x paksus: 175x231x15 mm, kaal: 739 g, 310 p., 1 Paperback / softback
  • Ilmumisaeg: 01-Oct-2017
  • Kirjastus: Oxford University Press Inc
  • ISBN-10: 1605357103
  • ISBN-13: 9781605357102
Teised raamatud teemal:
Püsilink: https://www.kriso.ee/db/9781605357102.html
Märksõnad:
Published by Sinauer Associates, an imprint of Oxford University Press.

Phylogenetic Trees Made Easy, Fifth Edition helps the reader get started in creating phylogenetic trees from protein or nucleic acid sequence data.

Although aimed at molecular and cell biologists, who may not be familiar with phylogenetic or evolutionary theory, it also serves students who have a theoretical understanding of phylogenetics but need guidance in transitioning to a practical application of the methodology. The reader is led, step by step, through identifying and acquiring the sequences to be included in a tree, aligning the sequences, estimating the tree by one of several methods, and drawing the tree for presentation to an intended audience. "Learn More" boxes present background on the various concepts and methods.
Chapter 1 Read Me First! 1(10)
New and Improved Software
2(1)
Just What Is a Phylogenetic Tree?
2(2)
Estimating Phylogenetic Trees: The Basics
4(1)
Beyond the Basics
5(2)
Learn More about the Principles
7(1)
About Appendix VI: F.A.Q.
7(1)
Computer Programs and Where to Obtain Them
8(1)
MEGA 7
8(1)
BEAST
8(1)
FigTree
8(1)
codeml
9(1)
SplitsTree and Dendroscope
9(1)
Graphviz
9(1)
Utility Programs
9(1)
Text Editors
9(1)
Acknowledging Computer Programs
9(1)
The Phylogenetic Trees Made Easy Website
10(1)
Chapter 2 Tutorial: Estimate a Tree 11(22)
Why Create Phylogenetic Trees?
11(1)
About this Tutorial
12(1)
Macintosh and Linux users
12(1)
A word about screen shots
12(1)
Search for Sequences Related to Your Sequence
13(5)
Decide Which Related Sequences to Include on Your Tree
18(4)
Establishing homology
19(1)
To include or not to include, that is the question
20(2)
Download the Sequences
22(5)
Align the Sequences
27(1)
Make a Neighbor Joining Tree
28(4)
Summary
32(1)
Chapter 3 Acquiring the Sequences 33(20)
Background
33(1)
Problems arising from the vast size of the sequence databases
33(1)
The query sequences
34(1)
Hunting Homologs: What Sequences Can Be Included on a Single Tree?
34(1)
Becoming More Familiar with BLAST
35(1)
BLAST help
36(1)
Using the Nucleotide BLAST Page
36(3)
Using BLAST to Search for Related Protein Sequences
39(4)
Finalizing Selected Sequences for a Tree
43(4)
Problems adding coding sequences of protein homologs to the Alignment Explorer
43(4)
Adding Sequences to and Removing Sequences from the Alignment Explorer
47(1)
Add a sequence
47(1)
Import a file of sequences
48(1)
Delete a sequence
48(1)
Other Ways to Find Sequences of Interest (Beware! The Risks Are High)
48(5)
Chapter 4 Aligning the Sequences 53(18)
Aligning Sequences with MUSCLE
53(4)
Examine and Possibly Manually Adjust the Alignment
57(3)
Trim excess sequence
57(1)
Eliminate duplicate sequences
58(2)
Check Average Identity to Estimate Reliability of the Alignment
60(2)
Codons: Pairwise amino acid identity
60(1)
Non-coding DNA sequences
61(1)
Increasing Alignment Speed by Adjusting MUSCLE'S Parameter Settings
62(2)
How MUSCLE works
62(1)
Adjusting parameters to increase alignment speed
63(1)
Aligning Sequences with ClustalW
64(1)
Aligning Sequences with GUIDANCE2
65(6)
Viewing the results
67(1)
Eliminate unreliable parts of the alignment
68(2)
Saving the GUIDANCE2 alignment
70(1)
Chapter 5 Major Methods for Estimating Phylogenetic Trees 71(6)
Learn More About Tree-Searching Methods
72(2)
Distance versus Character-Based Methods
74(3)
Learn More About Distance Methods
74(3)
Chapter 6 Neighbor Joining Trees 77(24)
Using MEGA7 to Estimate a Neighbor Joining Tree
77(3)
Learn More About Phylogenetic Trees
78(2)
Determine the suitability of the data for a Neighbor Joining tree
80(1)
Estimate the tree
81(7)
Learn More About Evolutionary Models
83(5)
Unrooted and Rooted Trees
88(3)
Estimating the Reliability of a Tree
91(8)
Learn More About Estimating The Reliability Of Phylogenetic Trees
92(7)
What about Protein Sequences?
99(2)
Chapter 7 Drawing Phylogenetic Trees 101(20)
Changing the Appearance of a Tree
101(11)
The Options dialog
104(4)
Branch styles
108(1)
Fine-tuning the appearance of a tree
109(3)
Rooting a Tree
112(2)
Finding an outgroup
112(2)
Subtrees
114(4)
Saving Trees
118(1)
Saving a tree description
118(1)
Saving a tree image
119(1)
Captions
119(2)
Chapter 8 Parsimony 121(20)
Learn More About Parsimony
121(2)
MP Search Methods
123(2)
Using SeaView for Parsimony
125(16)
Estimating a bootstrap tree in SeaView
133(3)
Using MEGA to draw the tree estimated by SeaView
136(5)
Chapter 9 Maximum Likelihood 141(10)
Learn More About Maximum Likelihood
141(2)
ML Analysis Using MEGA
143(5)
Test alternative models
144(4)
Estimating the Reliability of an ML Tree by Bootstrapping
148(1)
What about Protein Sequences?
149(2)
Chapter 10 Bayesian Inference of Trees Using BEAST 151(24)
BEAST: An Overview
151(1)
Installing BEAST
152(1)
Prepare the Input Alignment File
152(1)
Run BEAUti
153(9)
Learn More About Bayesian Inference
158(4)
Running BEAST
162(3)
Run Tracer
165(3)
Burnin
166(2)
Run TreeAnnotator
168(1)
What about Protein Sequences?
169(1)
Visualizing the BEAST Tree
170(5)
The icons above the tree
172(3)
Chapter 11 Which Method Should You Use? 175(8)
Criteria to Consider
175(3)
Accuracy
176(1)
Ease of interpretation
176(1)
Time and convenience
176(2)
Results of the Major Methods
178(5)
Chapter 12 Working with Various Computer Platforms 183(8)
Command-line Programs
183(1)
MEGA on the Macintosh Platform
184(4)
Navigating among folders on the Mac
184(4)
Printing trees and text from MEGA
188(1)
The Line Endings Issue
188(1)
Running the Utility Programs
189(2)
Chapter 13 Phylogenetic Networks 191(24)
Why Trees Are Not Always Sufficient
191(1)
Unrooted and Rooted Phylogenetic Networks
192(6)
Learn More About Phylogenetic Networks
193(5)
Using SplitsTree to Estimate Unrooted Phylogenetic Networks
198(13)
Estimating networks from alignments
198(6)
Rooting an unrooted network
204(1)
Estimating networks from trees
205(1)
Consensus networks
206(4)
Supernetworks
210(1)
Using Dendroscope to Estimate Rooted Networks from Rooted Trees
211(4)
Chapter 14 Minimum Spanning Trees 215(16)
Minimum Spanning Trees Are Not Phylogenetic Trees!
215(1)
Why Use Minimum Spanning Trees?
215(1)
Origin of MSTs and the Issue of Reliability
216(1)
What is a minimum spanning tree?
216(1)
Using MSTgold to Estimate MSTs
217(6)
The MSTgold input files
218(1)
Two ways for MSTgold to calculate the initial distance matrix
219(1)
Running MSTgold with the ebgC data
219(1)
The MSTgold output
220(3)
Bootstrapping MSTgold
223(2)
Exporting MSTs from Graphviz
225(1)
An Alternative Data Set to Illustrate Some Additional Features of MSTgold
226(3)
An Alternative to Graphviz: Hypercube
229(2)
Chapter 15 Time Trees 231(14)
Preparations to Estimate a Time Tree
231(3)
Estimating a Time Tree
234(4)
Viewing the Relative Time Tree
238(2)
An Absolute Time Tree
240(4)
Effect of more calibration points on absolute time trees
244(1)
Postscript
244(1)
Chapter 16 Reconstructing Ancestral Sequences 245(14)
Using MEGA to Estimate Ancestral Sequences by Maximum Likelihood
246(11)
Create the alignment
246(1)
Construct the phylogeny
246(1)
Examine the ancestral states at each site in the alignment
247(3)
Estimate the ancestral sequence
250(6)
Calculating the ancestral protein sequence and amino acid probabilities
256(1)
How Accurate Are the Estimated Ancestral Sequences?
257(2)
Chapter 17 Detecting Adaptive Evolution 259(22)
Effect of Alignment Accuracy on Detecting Adaptive Evolution
261(1)
Using MEGA to Detect Adaptive Evolution
261(5)
Why ebgC is an interesting example for considering adaptive evolution
261(1)
Detecting overall selection
261(2)
Detecting selection between pairs
263(1)
Finding the region of the gene that has been subject to positive selection
264(2)
Using codeml to Detect Adaptive Evolution
266(12)
Installation
267(2)
Run codeml
269(4)
Questions that underlie the models
273(2)
A closer look at ebgC_1.out
275(3)
Summary
278(1)
Postscript
278(3)
Compiling PAML yourself and running codeml without PAMLX
278(3)
Chapter 18 Estimating Phylogenetic Trees from Whole Genome Sequences 281(16)
The Pan-Genome Problem
282(1)
kSNP: An Alternative to Genome Alignment
282(2)
kSNP 2.0
284(2)
kChooser
284(1)
FCK
285(1)
Tree accuracy
286(1)
Always run kChooser before running kSNP
286(1)
Using kSNP3
286(11)
The steps in estimating phylogenetic trees from WGS using kSNP3
287(10)
Chapter 19 Some Final Advice: Learn to Program 297(42)
Appendix I File Formats and Their Interconversion
299(8)
Format Descriptions
299(6)
The MEGA format
299(1)
The FASTA format
300(1)
The Nexus format
301(3)
The PHYLIP format
304(1)
Interconverting Formats
305(2)
FastaConvert, MEGA, and Sea View
305(2)
Appendix II Text Editors
307(4)
Mac OS X: TextWrangler
307(1)
Windows: Notepad++
308(1)
Linux: Gedit
308(3)
Appendix Ill The Command-line Environment
311(8)
Introduction and History
311(1)
Terminal and Command Prompt: The Apps for Accessing the Command-line Environment
312(1)
The current directory
313(1)
Entering Commands
313(1)
Navigating in Terminal
314(2)
The Magic Trick
315(1)
What Is in the CWD? The is Command (§ dir)
316(1)
The-I option
317(1)
The-a option
317(1)
The permissions column
318(1)
The chmod command
318(1)
§The dir Command in Command Prompt
319(1)
Some Other Important Commands
320(3)
Copy a file
320(1)
Move a file
321(1)
Rename a file
321(1)
Make a directory
321(1)
Remove a directory
321(1)
Remove a file
321(1)
Print the contents of a file to the screen
321(1)
Clear the screen
321(2)
Appendix IV Installing and Running Command-line Programs
323(8)
Installing Command-line Programs
323(6)
Mac OS X/Linux
323(1)
Windows
324(5)
Running Command-line Programs
329(2)
An example
330(1)
The line endings issue
330(1)
The example command line
330(1)
The output file(s)
330(1)
Error checking
330(1)
Appendix V Additional Programs
331(4)
Appendix VI Frequently Asked Questions
335(4)
Literature Cited 339(2)
Index to Major Program Discussions 341(4)
Subject Index 345
Barry G. Hall is Director of the Bellingham Research Institute, Adjunct Professor of Genomics and Bioinformatics at the Allegheny-Singer Research Institute's Center for Genomic Sciences, and Professor Emeritus of Biology, University of Rochester. A founding member of the Society for Molecular Biology and Evolution, he has served as Editor-in-Chief of its journal, Molecular Biology and Evolution, and on the Editorial Boards of Genetics, the Journal of Molecular Evolution, and the Journal of Bacteriology. His current research interests include the molecular epidemiology of bacterial pathogens and application of genomic analysis to rapid prediction of antibiotic sensitivity in clinical applications. He has continued to publish 2-3 papers a year since his retirement in 2003.