Phylogenetic trees made easy: a how-to manual
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Sunderland, Mass.
Sinauer
2004
|
| Edition: | 2. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIII,221 S. zahlr. Ill., graph. Darst. 1 CD-ROM |
| ISBN: | 0878933123 |
Staff View
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| 245 | 1 | 0 | |a Phylogenetic trees made easy |b a how-to manual |c Barry G. Hall |
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| adam_text | Table of Contents
Introduction: Read Me First 1
A Brief Overview of the Second Edition 2
Time Limited Copy of the PAUP*4.0 Program 3
Learn More about the Principles 4
Computer Programs Discussed and Where to Obtain Them 4
ClustalX 5
Tree View 5
PAUP* 5
PHYLIP (PHYLogeny Inference Package) 6
Tree Puzzle 6
MrBayes 7
CodonAlign 7
Other Programs 7
Files and Utilities on the Phylogenetics Made Easy
Website and CD 7
Some Conventions Used in This Book 8
Chapter 1 Tutorial: Create a Tree! 9
Why Create Phylogenetic Trees? 9
Obtaining Related Sequences by a BLAST Search 10
Step 1: Go to the BLAST Website 11
Step 2: Use BLAST to Search for Sequences Related to Your
Sequence 13
Step 3: Decide Which Related Sequences to Include on Your Tree 14
Downloading the Selected Sequences 20
x Table of Contents
Creating the Multiple Alignment 23
Creating the Input File 24
Getting the Data into ClustalX 26
Some General Comments about Creating Alignments 27
Setting the Alignment Parameters 27
Creating the Alignment 32
Refining and Improving the Alignment 33
Aligning New Sequences to an Existing Alignment, or Aligning
Two Existing Alignments 38
Phylogenetic Analysis 40
Exactly What Is a Phylogenetic Tree? 41
Methods for Constructing Phylogenies 41
LEARN MORE ABOUT PHYLOCENETIC TREES 42
Using ClustalX to Create a Neighbor Joining Tree 46
Drawing the Tree Using Tree View 47
Tree Formats: Different Appearances of the Same Tree 47
Bootstrapping a Tree 50
LEARN MORE ABOUT ESTIMATING THE RELIABILITY OF PHYLOGENETIC TREES 52
Placing the Root of a Tree 53
LEARNG MORE ABOUT ROOTING PHYLOGENETIC TREES 56
Printing and Saving the Tree 59
Summary 60
Chapter 2 Basic Elements in Creating and
Presenting Trees 61
Selecting Homologs: What Sequences Can Be Put on a
Single Tree? 61
Fine Tuning Alignments 64
Major Methods for Creating Trees 68
Which Method Should You Use? 68
Distance versus Character Based Methods 69
LEARN MORE ABOUT TREE SEARCHING METHODS 70
LEARN MORE ABOUT DISTANCE METHODS 74
Data Files Used to Illustrate Methods 76
Table of Contents xi
Using PAUP* to Create Trees 76
Opening the Input File 77
Creating Neighbor Joining Trees Using PAUP* 80
Creating Parsimony Trees Using PAUP* 92
LEARN MORE ABOUT PARSIMONY 94
Creating a Consensus Tree Using PAUP* 100
Creating Maximum Likelihood DNA Trees Using PAUP* 102
LEARN MORE ABOUT MAXIMUM LIKELIHOOD 1 04
LEARN MORE ABOUT EVOLUTIONARY METHODS 110
Creating Maximum Likelihood Protein Trees Using Tree Puzzle 114
Creating Bayesian Trees Using MrBayes 118
Creating the Execution File 119
LEARN MORE ABOUT BAYESIAN ANALYSIS 120
What the Statements in the Example MrBayes Block Do 123
Interpreting MrBayes Results 128
Sample Blocks for MrBayes 130
Getting Help 132
Presenting and Printing Your Trees 135
Opening Tree Files in PAUP* 135
To Root or Not to Root? 139
Choosing What Form of a Tree to Publish 147
Making a Tree Pretty: Not Just a Cosmetic Matter 148
DNA Phylogeny or Protein Phylogeny: Which Is Better? 152
Using CodonAlign 2.0 154
Chapter 3 Advanced Elements in Constructing
Trees 157
Reconstructing Ancestral DNA Sequences 157
Ancestral Sequences for Parsimony and Maximum Likelihood Trees
Using PAUP* 158
Ancestral Sequences for Parsimony using PHYLIP 161
Using Protein Structure Information to Construct Very Deep
Phytogenies 167
Analyzing Trees for Evidence of Adaptive Evolution by Detecting
Positive Selection in a Phylogeny 173
xii Table of Contents
Chapter 4 Using Alternative Software to Construct
and Present Trees 179
Using PAUP* with Windows or Unix 179
Opening and Viewing Files 180
Using PAUP Blocks 182
Bootstrapping 185
Using PHYLIP 187
General Features of PHYLIP Programs 188
Parsimony Trees 189
Consensus Trees 190
Neighbor Joining Trees 190
Maximum Likelihood Trees 191
Bootstrapping 191
Appendix I File Formats and Their
Interconversion 193
Formats Used by Programs Discussed in this Book 193
The FASTA Format 193
The Clustal Format 194
The Nexus Format 195
PHYLIP 3.x 197
Other File Formats 199
The GCG/MSF Format and PileUp 199
The NBRF/PIR format 200
Interconverting Formats Using PAUP* 201
Importing Various File Formats into PAUP* 201
Exporting Various File Formats from PAUP* 202
Interconverting Interleaved and Sequential Formatted
PHYLIP Files 203
Table of Contents xiii
Appendix II Printing Alignments 205
Printing to Assess the Quality of the Alignment 205
Printing Alignments for Publication 206
Literature Cited 207
Index to Major Programs Discussed 209
Subject Index 215
|
| adam_txt |
Table of Contents
Introduction: Read Me First 1
A Brief Overview of the Second Edition 2
Time Limited Copy of the PAUP*4.0 Program 3
Learn More about the Principles 4
Computer Programs Discussed and Where to Obtain Them 4
ClustalX 5
Tree View 5
PAUP* 5
PHYLIP (PHYLogeny Inference Package) 6
Tree Puzzle 6
MrBayes 7
CodonAlign 7
Other Programs 7
Files and Utilities on the "Phylogenetics Made Easy"
Website and CD 7
Some Conventions Used in This Book 8
Chapter 1 Tutorial: Create a Tree! 9
Why Create Phylogenetic Trees? 9
Obtaining Related Sequences by a BLAST Search 10
Step 1: Go to the BLAST Website 11
Step 2: Use BLAST to Search for Sequences Related to Your
Sequence 13
Step 3: Decide Which Related Sequences to Include on Your Tree 14
Downloading the Selected Sequences 20
x Table of Contents
Creating the Multiple Alignment 23
Creating the Input File 24
Getting the Data into ClustalX 26
Some General Comments about Creating Alignments 27
Setting the Alignment Parameters 27
Creating the Alignment 32
Refining and Improving the Alignment 33
Aligning New Sequences to an Existing Alignment, or Aligning
Two Existing Alignments 38
Phylogenetic Analysis 40
Exactly What Is a Phylogenetic Tree? 41
Methods for Constructing Phylogenies 41
LEARN MORE ABOUT PHYLOCENETIC TREES 42
Using ClustalX to Create a Neighbor Joining Tree 46
Drawing the Tree Using Tree View 47
Tree Formats: Different Appearances of the Same Tree 47
Bootstrapping a Tree 50
LEARN MORE ABOUT ESTIMATING THE RELIABILITY OF PHYLOGENETIC TREES 52
Placing the Root of a Tree 53
LEARNG MORE ABOUT ROOTING PHYLOGENETIC TREES 56
Printing and Saving the Tree 59
Summary 60
Chapter 2 Basic Elements in Creating and
Presenting Trees 61
Selecting Homologs: What Sequences Can Be Put on a
Single Tree? 61
Fine Tuning Alignments 64
Major Methods for Creating Trees 68
Which Method Should You Use? 68
Distance versus Character Based Methods 69
LEARN MORE ABOUT TREE SEARCHING METHODS 70
LEARN MORE ABOUT DISTANCE METHODS 74
Data Files Used to Illustrate Methods 76
Table of Contents xi
Using PAUP* to Create Trees 76
Opening the Input File 77
Creating Neighbor Joining Trees Using PAUP* 80
Creating Parsimony Trees Using PAUP* 92
LEARN MORE ABOUT PARSIMONY 94
Creating a Consensus Tree Using PAUP* 100
Creating Maximum Likelihood DNA Trees Using PAUP* 102
LEARN MORE ABOUT MAXIMUM LIKELIHOOD 1 04
LEARN MORE ABOUT EVOLUTIONARY METHODS 110
Creating Maximum Likelihood Protein Trees Using Tree Puzzle 114
Creating Bayesian Trees Using MrBayes 118
Creating the Execution File 119
LEARN MORE ABOUT BAYESIAN ANALYSIS 120
What the Statements in the Example MrBayes Block Do 123
Interpreting MrBayes Results 128
Sample Blocks for MrBayes 130
Getting Help 132
Presenting and Printing Your Trees 135
Opening Tree Files in PAUP* 135
To Root or Not to Root? 139
Choosing What Form of a Tree to Publish 147
Making a Tree Pretty: Not Just a Cosmetic Matter 148
DNA Phylogeny or Protein Phylogeny: Which Is Better? 152
Using CodonAlign 2.0 154
Chapter 3 Advanced Elements in Constructing
Trees 157
Reconstructing Ancestral DNA Sequences 157
Ancestral Sequences for Parsimony and Maximum Likelihood Trees
Using PAUP* 158
Ancestral Sequences for Parsimony using PHYLIP 161
Using Protein Structure Information to Construct Very Deep
Phytogenies 167
Analyzing Trees for Evidence of Adaptive Evolution by Detecting
Positive Selection in a Phylogeny 173
xii Table of Contents
Chapter 4 Using Alternative Software to Construct
and Present Trees 179
Using PAUP* with Windows or Unix 179
Opening and Viewing Files 180
Using PAUP Blocks 182
Bootstrapping 185
Using PHYLIP 187
General Features of PHYLIP Programs 188
Parsimony Trees 189
Consensus Trees 190
Neighbor Joining Trees 190
Maximum Likelihood Trees 191
Bootstrapping 191
Appendix I File Formats and Their
Interconversion 193
Formats Used by Programs Discussed in this Book 193
The FASTA Format 193
The Clustal Format 194
The Nexus Format 195
PHYLIP 3.x 197
Other File Formats 199
The GCG/MSF Format and PileUp 199
The NBRF/PIR format 200
Interconverting Formats Using PAUP* 201
Importing Various File Formats into PAUP* 201
Exporting Various File Formats from PAUP* 202
Interconverting Interleaved and Sequential Formatted
PHYLIP Files 203
Table of Contents xiii
Appendix II Printing Alignments 205
Printing to Assess the Quality of the Alignment 205
Printing Alignments for Publication 206
Literature Cited 207
Index to Major Programs Discussed 209
Subject Index 215 |
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| genre | Lehrbuch - CAD - Phylogenetische Systematik - Stammbaum |
| genre_facet | Lehrbuch - CAD - Phylogenetische Systematik - Stammbaum |
| id | DE-604.BV020872231 |
| illustrated | Illustrated |
| index_date | 2024-07-02T13:26:28Z |
| indexdate | 2024-07-09T20:27:10Z |
| institution | BVB |
| isbn | 0878933123 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-014193954 |
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| publisher | Sinauer |
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| spelling | Hall, Barry G. Verfasser aut Phylogenetic trees made easy a how-to manual Barry G. Hall 2. ed. Sunderland, Mass. Sinauer 2004 XIII,221 S. zahlr. Ill., graph. Darst. 1 CD-ROM txt rdacontent n rdamedia nc rdacarrier Datenverarbeitung - Molekularbiologie - Phylogenetik Datenverarbeitung Phylogeny Data processing Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Phylogenetik (DE-588)4174591-7 gnd rswk-swf Phylogenie (DE-588)4076110-1 gnd rswk-swf Phylogenetische Systematik (DE-588)4174592-9 gnd rswk-swf Datenverarbeitung (DE-588)4011152-0 gnd rswk-swf Lehrbuch - CAD - Phylogenetische Systematik - Stammbaum Phylogenie (DE-588)4076110-1 s Datenverarbeitung (DE-588)4011152-0 s DE-604 Phylogenetik (DE-588)4174591-7 s Molekularbiologie (DE-588)4039983-7 s Phylogenetische Systematik (DE-588)4174592-9 s 1\p DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014193954&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Hall, Barry G. Phylogenetic trees made easy a how-to manual Datenverarbeitung - Molekularbiologie - Phylogenetik Datenverarbeitung Phylogeny Data processing Molekularbiologie (DE-588)4039983-7 gnd Phylogenetik (DE-588)4174591-7 gnd Phylogenie (DE-588)4076110-1 gnd Phylogenetische Systematik (DE-588)4174592-9 gnd Datenverarbeitung (DE-588)4011152-0 gnd |
| subject_GND | (DE-588)4039983-7 (DE-588)4174591-7 (DE-588)4076110-1 (DE-588)4174592-9 (DE-588)4011152-0 |
| title | Phylogenetic trees made easy a how-to manual |
| title_auth | Phylogenetic trees made easy a how-to manual |
| title_exact_search | Phylogenetic trees made easy a how-to manual |
| title_exact_search_txtP | Phylogenetic trees made easy a how-to manual |
| title_full | Phylogenetic trees made easy a how-to manual Barry G. Hall |
| title_fullStr | Phylogenetic trees made easy a how-to manual Barry G. Hall |
| title_full_unstemmed | Phylogenetic trees made easy a how-to manual Barry G. Hall |
| title_short | Phylogenetic trees made easy |
| title_sort | phylogenetic trees made easy a how to manual |
| title_sub | a how-to manual |
| topic | Datenverarbeitung - Molekularbiologie - Phylogenetik Datenverarbeitung Phylogeny Data processing Molekularbiologie (DE-588)4039983-7 gnd Phylogenetik (DE-588)4174591-7 gnd Phylogenie (DE-588)4076110-1 gnd Phylogenetische Systematik (DE-588)4174592-9 gnd Datenverarbeitung (DE-588)4011152-0 gnd |
| topic_facet | Datenverarbeitung - Molekularbiologie - Phylogenetik Datenverarbeitung Phylogeny Data processing Molekularbiologie Phylogenetik Phylogenie Phylogenetische Systematik Lehrbuch - CAD - Phylogenetische Systematik - Stammbaum |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014193954&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT hallbarryg phylogenetictreesmadeeasyahowtomanual |