Phylogenetic trees made easy: a how-to manual
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Sunderland, Mass.
Sinauer
2008
|
| Ausgabe: | 3. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIV, 233 S. Ill., graph. Darst. |
| ISBN: | 9780878933105 |
Internformat
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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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| 264 | 1 | |a Sunderland, Mass. |b Sinauer |c 2008 | |
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Datensatz im Suchindex
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|---|---|
| adam_text | TABLE OF CONTENTS CHAPTERI READ ME FIRST! 1 A BRIEF OVERVIEW I NEW AND
IMPROVED SOFTWARE 2 THE EASY STEPS TO MAKING A TREE 2 LEARN MORE ABOUT
THE PRINCIPLES 4 COMPUTER PROGRAMS DISCUSSED AND WHERE TO OBTAIN THEM 4
MEGA 5 PHYML 5 MRBAYES 5 CODEMI 5 UTILITY PROGRAMS 6 MACINTOSH ONLY! 6
THE PHYLOGENETIC TREES MADE EASY WEBSITE 6 REGISTER FOR UPDATED
INFORMATION 7 SOME CONVENTIONS USED IN THIS BOOK 7 CHAPTER 2 TUTORIAL:
CREATE A TREE! 9 WHYCREATE PHYLOGENETIC TREES? G ABOUT THIS TUTORIAL 10
MEGA W OBTAINING RETATED SEQUENCES BY A BLAST SEARCH 11 STEP 1: USE
BLAST TO SEARCH FOR SEQUENCES RELATED TO YOUR SEQUENCE 12 STEP 2: DECIDE
WHICH RELATED SEQUENCES TO INCLUDE ON YOUR TREE 14 STEP 3: DOWNLOAD THE
SEQUENCE 18 ALIGNING THE SEQUENCES 22 MAKE A NEIGHBOR-JOINING TREE 25
SUMMARY 29 X TABIE OF CONTENTS CHAPTER 3 ACQUIRING AND ALIGNING THE
SEQUENCES 31 SEIECTING HOMOLOGS: WHAT SEQUENCES CAN BE PUTONTO A SINGLE
TREE? 31 FINDING HOMOLOGOUS SEQUENCES BY A BLAST SEARCH 32 OTHER WAYS TO
FIND SEQUENCES OF INTEREST: BEWARE! THE RISKS ARE HIGH 40 ALIGNING THE
SEQUENCES 45 ELIMINATE DUPLICATE SEQUENCES 51 ELIMINATE OBVIOUSLY WRONG
SEQUENCES 53 CHECK AVERAGE AMINO ACID IDENTITY TO ESTIMATE RELIABILITY
OF THE ALIGNMENT 55 NON-CODING DNA SEQUENCES 56 INTERLUDE I MAJOR
METHODS FOR ESTIMATING PHYLOGENETICTREES 57 LEARN MORE ABOUT
TREE-SEARCHING METHODS 58 DISTANCE VERSUS CHARACTER-BASED METHODS 60
DATA FITES USED TO LUEUSTRATE METHODS 61 CHAPTER 4 NEIGHBOR-JOINING TREES
63 DETERMINE THE SUITABILITY OF THE DATA FOR A NEIGHBOR-JOINING TREE 63
LEARN MORE ABOUT DISTANCE METHODS 65 LEARN MORE ABOUT PHYLOGENETTC TREES
67 ESTIMATE THE NEIGHBOR-JOINING TREE 70 LEARN MORE ABOUT EVOLUTIONARY
MODELS 75 ESTIMATING THE RELIABILITY OF A TREE 80 LEARN MORE ABOUT
ESTIMATING THE RELIABILITY OF PHYLOGENETIC TREES 81 WHAT ABOUT PROTEIN
SEQUENCES? 88 CHAPTER 5 DRAWING PHYLOGENETIC TREES 89 CHANGING THE
APPEARANCE OFA TREE 89 ROOTING 0 TREE 99 FINDING AN OUTGROUP 101
SUBTREES 103 SAVING TREES 105 CAPTIONS 106 CHAPTER 6 PARSIMONY 109
SEARCH METHODS 110 LEARN MORE ABOUT PARSIMONY 112 MULTIPLE EQUALLY
PARSIMONIOUS TREES 115 BRANCH LENGTHS 117 LEVEL OFCNI SEARCH 118
CONSENSUS AND BOOTSTRAP TREES 118 WHAT ABOUT PROTEIN SEQUENCES? 123
CHAPTER 7 MAXIMUM LIKELIHOOD 125 SAVING THE DATA IN THE PHYLIP FORMAT
125 LEARN MORE ABOUT MAXIMUM LIKELIHOOD 126 INSTALLING AND STARTING
PHYML 129 RUNNING PHYML 130 IMPORTING THE ML TREE DESCRIPTION INTO MEGA
AND DRAWING THE TREE 132 TREE RELIABILITY ESTIMATED BY THE APPROXIMATE
LIKELIHOOD RATIO TEST METHOD(ALRT) 136 LEARN MORE ABOUT ALRT 137 THE
SPECIAL CASE OFZERO LENGTH BRANCHES 139 TEST ALTERNATIVE MODELS 140 WHAT
ABOUT PROTEIN SEQUENCES? 141 CHAPTER 8 BAYESIAN INFERENCE OF TREES WITH
MRBAYES 143 LEARN MORE ABOUT BAYESIAN ANALYSIS 144 CREATING THE
EXECUTION FILE 146 WHAT THE STATEMENTS IN THE EXAMPIE MRBAYES BLOCK DO
148 WHAT HAPPENS DURING MRBAYES ANALYSIS? 149 THE SUMT COMMAND 152 WHAT
IFYOU DON T GET CONVERGENCE? 152 VISUALIZING THE MRBAYES TREE 154 WHAT
ABOUT PROTEIN SEQUENCES? 157 FORTHCOMING VERSION OF MRBAYES 157
INTERLUDE II WHICH METHOD SHOULD YOU USE? 159 ACCURACY 160 EASE OF
INTERPRETATION 160 TIME AND CONVENIENCE 161 DIFFERENT ESTIMATES OFTREE
RELIABILITY 162 CHAPTER 9 RECONSTRUCTING ANCESTRAL SEQUENCES 165 USING
MRBAYES TO ESTIMATE ANCESTRAL SEQUENCES 166 THE ALIGNMENT 166 CONSTRUCT
THE PHYLOGENY 166 ESTIMATE THE ANCESTRAL SEQUENCE 166 MAKING SENSE OF
THE SUMP.ANC FILE 169 CONECTING ANCESTRAL SEQUENCES FOR ANCESTRAL GAPS
173 THE EMERGENCY SUMP PROGRAM. 174 THE CORRECTED SEQUENCE 176 WHAT
ABOUT THE UNRELIABLE SITES? 176 CHAPTENO DETECTINGADAPTIVE EVOLUTION 177
USING MEGA TO DETECT ADAPTIVE EVOLUTION 178 USING CODEMI TO DETECT
ADOPTIVE EVOLUTION 183 WINDOWS INSTALLATION 183 MACINTOSH OSX
INSTALLATION 183 UNIX/LINUX USERS 183 THE FILES YOU NEED TO RUN CODEMI
183 THE CODEMI CONTROL FILE 184 QUESTIONSTHATUNDERLIE THE MODELS 184 RUN
CODEMI 186 IDENTIFY THE BRANCHES ALONG WHICH SELECTION MAY HAVE OCCURRED
186 TEST THE STATISTICAL SIGNIFICANCE OF THE DN/DS RATIOS 186 CHAPTER 11
WORKING WITH VARIOUS COMPUTER PLATFORMS 189 THE LINE ENDINGS ISSUE 189
MEGA FOR MACINTOSH USERS 190 PPC-BASED MACS 190 INTEL-BASED MACS 191
DOWNLOAD AND INSTALL MEGA 191 MEGA FOR UNIX/LINUX USERS 191 MEGA FOR
WINDOWS USERS 191 WINDOWS USERS: CREATE A BIN FOLDER AND 0 PATH TO IT
192 A BRIEF VISIT TO THE COMMAND PROMPT PROGRAM FOR WINDOWS USERS 194 A
BRIEF VISIT TO UNIX FOR MACINTOSH USERS 196 PHYML FOR WINDOWS USERS 197
PHYML FOR MACINTOSH USERS 198 INSTALL PHYML 198 PHYML FOR UNIX/LINUX
USERS 198 MRBAYES FOR WINDOWS USERS 198 MRBAYES FOR MACINTOSH USERS 199
COMPILE MRBAYES FOR YOUR MAC 199 USING THE MRBAYES BINARY 199 MRBAYES
FOR UNIX/LINUX USERS 200 UTILITY PROGRAMS FOR WINDOWS USERS 200
INSTALLING THE UTILITY PROGRAMS 200 RUNNING THE UTILITY PROGRAMS 200
UTILITY PROGRAMS FOR MACINTOSH USERS 200 INSTALLING THE UTILITY PROGRAMS
200 RUNNING THE UTILITY PROGRAMS 201 UTILITY PROGRAMS FOR LINUX AND UNIX
USERS 201 COMPILING THE UTILITY PROGRAMS 201 RUNNING THE UTILITY
PROGRAMS 201 SPECIFIC INSTRUCTIONS FOR THE UTILITY PROGRAMS IN THE
DOWNLOAD PACKAGES 202 APPENDIX I FILE FORMATS AND THEIR INTERCONVERSION
205 FORMATS USED BY PROGRAMS DISCUSSED IN THIS BOOK 205 THE MEGA FORMAT
205 THE FASTA FORMAT 206 THE NEXUS FORMAT 207 PHYLIP 209 OTHER FILE
FORMATS 211 THE GCG/MSF FORMAT 211 PILEUP 211 THE NBRF/PIR FORMAT 212
INTERCONVERTING FORMATS 213 APPENDIX II ADDITIONAL PROGRAMS 215
LITERATURE CITED 221 INDEX TO MAJOR PROGRAMS DISCUSSED 223 SUBJECT INDEX
229
|
| adam_txt |
TABLE OF CONTENTS CHAPTERI READ ME FIRST! 1 A BRIEF OVERVIEW I NEW AND
IMPROVED SOFTWARE 2 THE EASY STEPS TO MAKING A TREE 2 LEARN MORE ABOUT
THE PRINCIPLES 4 COMPUTER PROGRAMS DISCUSSED AND WHERE TO OBTAIN THEM 4
MEGA 5 PHYML 5 MRBAYES 5 CODEMI 5 UTILITY PROGRAMS 6 MACINTOSH ONLY! 6
THE PHYLOGENETIC TREES MADE EASY WEBSITE 6 REGISTER FOR UPDATED
INFORMATION 7 SOME CONVENTIONS USED IN THIS BOOK 7 CHAPTER 2 TUTORIAL:
CREATE A TREE! 9 WHYCREATE PHYLOGENETIC TREES? G ABOUT THIS TUTORIAL 10
MEGA W OBTAINING RETATED SEQUENCES BY A BLAST SEARCH 11 STEP 1: USE
BLAST TO SEARCH FOR SEQUENCES RELATED TO YOUR SEQUENCE 12 STEP 2: DECIDE
WHICH RELATED SEQUENCES TO INCLUDE ON YOUR TREE 14 STEP 3: DOWNLOAD THE
SEQUENCE 18 ALIGNING THE SEQUENCES 22 MAKE A NEIGHBOR-JOINING TREE 25
SUMMARY 29 X TABIE OF CONTENTS CHAPTER 3 ACQUIRING AND ALIGNING THE
SEQUENCES 31 SEIECTING HOMOLOGS: WHAT SEQUENCES CAN BE PUTONTO A SINGLE
TREE? 31 FINDING HOMOLOGOUS SEQUENCES BY A BLAST SEARCH 32 OTHER WAYS TO
FIND SEQUENCES OF INTEREST: BEWARE! THE RISKS ARE HIGH 40 ALIGNING THE
SEQUENCES 45 ELIMINATE DUPLICATE SEQUENCES 51 ELIMINATE OBVIOUSLY WRONG
SEQUENCES 53 CHECK AVERAGE AMINO ACID IDENTITY TO ESTIMATE RELIABILITY
OF THE ALIGNMENT 55 NON-CODING DNA SEQUENCES 56 INTERLUDE I MAJOR
METHODS FOR ESTIMATING PHYLOGENETICTREES 57 LEARN MORE ABOUT
TREE-SEARCHING METHODS 58 DISTANCE VERSUS CHARACTER-BASED METHODS 60
DATA FITES USED TO LUEUSTRATE METHODS 61 CHAPTER 4 NEIGHBOR-JOINING TREES
63 DETERMINE THE SUITABILITY OF THE DATA FOR A NEIGHBOR-JOINING TREE 63
LEARN MORE ABOUT DISTANCE METHODS 65 LEARN MORE ABOUT PHYLOGENETTC TREES
67 ESTIMATE THE NEIGHBOR-JOINING TREE 70 LEARN MORE ABOUT EVOLUTIONARY
MODELS 75 ESTIMATING THE RELIABILITY OF A TREE 80 LEARN MORE ABOUT
ESTIMATING THE RELIABILITY OF PHYLOGENETIC TREES 81 WHAT ABOUT PROTEIN
SEQUENCES? 88 CHAPTER 5 DRAWING PHYLOGENETIC TREES 89 CHANGING THE
APPEARANCE OFA TREE 89 ROOTING 0 TREE 99 FINDING AN OUTGROUP 101
SUBTREES 103 SAVING TREES 105 CAPTIONS 106 CHAPTER 6 PARSIMONY 109
SEARCH METHODS 110 LEARN MORE ABOUT PARSIMONY 112 MULTIPLE EQUALLY
PARSIMONIOUS TREES 115 BRANCH LENGTHS 117 LEVEL OFCNI SEARCH 118
CONSENSUS AND BOOTSTRAP TREES 118 WHAT ABOUT PROTEIN SEQUENCES? 123
CHAPTER 7 MAXIMUM LIKELIHOOD 125 SAVING THE DATA IN THE PHYLIP FORMAT
125 LEARN MORE ABOUT MAXIMUM LIKELIHOOD 126 INSTALLING AND STARTING
PHYML 129 RUNNING PHYML 130 IMPORTING THE ML TREE DESCRIPTION INTO MEGA
AND DRAWING THE TREE 132 TREE RELIABILITY ESTIMATED BY THE APPROXIMATE
LIKELIHOOD RATIO TEST METHOD(ALRT) 136 LEARN MORE ABOUT ALRT 137 THE
SPECIAL CASE OFZERO LENGTH BRANCHES 139 TEST ALTERNATIVE MODELS 140 WHAT
ABOUT PROTEIN SEQUENCES? 141 CHAPTER 8 BAYESIAN INFERENCE OF TREES WITH
MRBAYES 143 LEARN MORE ABOUT BAYESIAN ANALYSIS 144 CREATING THE
EXECUTION FILE 146 WHAT THE STATEMENTS IN THE EXAMPIE MRBAYES BLOCK DO
148 WHAT HAPPENS DURING MRBAYES ANALYSIS? 149 THE SUMT COMMAND 152 WHAT
IFYOU DON' T GET CONVERGENCE? 152 VISUALIZING THE MRBAYES TREE 154 WHAT
ABOUT PROTEIN SEQUENCES? 157 FORTHCOMING VERSION OF MRBAYES 157
INTERLUDE II WHICH METHOD SHOULD YOU USE? 159 ACCURACY 160 EASE OF
INTERPRETATION 160 TIME AND CONVENIENCE 161 DIFFERENT ESTIMATES OFTREE
RELIABILITY 162 CHAPTER 9 RECONSTRUCTING ANCESTRAL SEQUENCES 165 USING
MRBAYES TO ESTIMATE ANCESTRAL SEQUENCES 166 THE ALIGNMENT 166 CONSTRUCT
THE PHYLOGENY 166 ESTIMATE THE ANCESTRAL SEQUENCE 166 MAKING SENSE OF
THE SUMP.ANC FILE 169 CONECTING ANCESTRAL SEQUENCES FOR ANCESTRAL GAPS
173 THE EMERGENCY SUMP PROGRAM. 174 THE CORRECTED SEQUENCE 176 WHAT
ABOUT THE UNRELIABLE SITES? 176 CHAPTENO DETECTINGADAPTIVE EVOLUTION 177
USING MEGA TO DETECT ADAPTIVE EVOLUTION 178 USING CODEMI TO DETECT
ADOPTIVE EVOLUTION 183 WINDOWS INSTALLATION 183 MACINTOSH OSX
INSTALLATION 183 UNIX/LINUX USERS 183 THE FILES YOU NEED TO RUN CODEMI
183 THE CODEMI CONTROL FILE 184 QUESTIONSTHATUNDERLIE THE MODELS 184 RUN
CODEMI 186 IDENTIFY THE BRANCHES ALONG WHICH SELECTION MAY HAVE OCCURRED
186 TEST THE STATISTICAL SIGNIFICANCE OF THE DN/DS RATIOS 186 CHAPTER 11
WORKING WITH VARIOUS COMPUTER PLATFORMS 189 THE LINE ENDINGS ISSUE 189
MEGA FOR MACINTOSH USERS 190 PPC-BASED MACS 190 INTEL-BASED MACS 191
DOWNLOAD AND INSTALL MEGA 191 MEGA FOR UNIX/LINUX USERS 191 MEGA FOR
WINDOWS USERS 191 WINDOWS USERS: CREATE A BIN FOLDER AND 0 PATH TO IT
192 A BRIEF VISIT TO THE COMMAND PROMPT PROGRAM FOR WINDOWS USERS 194 A
BRIEF VISIT TO UNIX FOR MACINTOSH USERS 196 PHYML FOR WINDOWS USERS 197
PHYML FOR MACINTOSH USERS 198 INSTALL PHYML 198 PHYML FOR UNIX/LINUX
USERS 198 MRBAYES FOR WINDOWS USERS 198 MRBAYES FOR MACINTOSH USERS 199
COMPILE MRBAYES FOR YOUR MAC 199 USING THE MRBAYES BINARY 199 MRBAYES
FOR UNIX/LINUX USERS 200 UTILITY PROGRAMS FOR WINDOWS USERS 200
INSTALLING THE UTILITY PROGRAMS 200 RUNNING THE UTILITY PROGRAMS 200
UTILITY PROGRAMS FOR MACINTOSH USERS 200 INSTALLING THE UTILITY PROGRAMS
200 RUNNING THE UTILITY PROGRAMS 201 UTILITY PROGRAMS FOR LINUX AND UNIX
USERS 201 COMPILING THE UTILITY PROGRAMS 201 RUNNING THE UTILITY
PROGRAMS 201 SPECIFIC INSTRUCTIONS FOR THE UTILITY PROGRAMS IN THE
DOWNLOAD PACKAGES 202 APPENDIX I FILE FORMATS AND THEIR INTERCONVERSION
205 FORMATS USED BY PROGRAMS DISCUSSED IN THIS BOOK 205 THE MEGA FORMAT
205 THE FASTA FORMAT 206 THE NEXUS FORMAT 207 PHYLIP 209 OTHER FILE
FORMATS 211 THE GCG/MSF FORMAT 211 PILEUP 211 THE NBRF/PIR FORMAT 212
INTERCONVERTING FORMATS 213 APPENDIX II ADDITIONAL PROGRAMS 215
LITERATURE CITED 221 INDEX TO MAJOR PROGRAMS DISCUSSED 223 SUBJECT INDEX
229 |
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| author | Hall, Barry G. 1942- |
| author_GND | (DE-588)133536041 |
| author_facet | Hall, Barry G. 1942- |
| author_role | aut |
| author_sort | Hall, Barry G. 1942- |
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| building | Verbundindex |
| bvnumber | BV022931875 |
| callnumber-first | Q - Science |
| callnumber-label | QH367 |
| callnumber-raw | QH367.5 |
| callnumber-search | QH367.5 |
| callnumber-sort | QH 3367.5 |
| callnumber-subject | QH - Natural History and Biology |
| classification_rvk | WC 5051 WH 6000 |
| ctrlnum | (OCoLC)255684370 (DE-599)BVBBV022931875 |
| dewey-full | 576.880285 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 576 - Genetics and evolution |
| dewey-raw | 576.880285 |
| dewey-search | 576.880285 |
| dewey-sort | 3576.880285 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| discipline_str_mv | Biologie |
| edition | 3. ed. |
| format | Book |
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| id | DE-604.BV022931875 |
| illustrated | Illustrated |
| index_date | 2024-07-02T18:54:51Z |
| indexdate | 2024-07-09T21:07:56Z |
| institution | BVB |
| isbn | 9780878933105 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016136687 |
| oclc_num | 255684370 |
| open_access_boolean | |
| owner | DE-20 DE-19 DE-BY-UBM DE-188 |
| owner_facet | DE-20 DE-19 DE-BY-UBM DE-188 |
| physical | XIV, 233 S. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Sinauer |
| record_format | marc |
| spelling | Hall, Barry G. 1942- Verfasser (DE-588)133536041 aut Phylogenetic trees made easy a how-to manual Barry G. Hall 3. ed. Sunderland, Mass. Sinauer 2008 XIV, 233 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Datenverarbeitung Phylogeny Data processing Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Phylogenetische Systematik (DE-588)4174592-9 gnd rswk-swf Phylogenie (DE-588)4076110-1 gnd rswk-swf Phylogenetik (DE-588)4174591-7 gnd rswk-swf Datenverarbeitung (DE-588)4011152-0 gnd rswk-swf 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 DE-188 OEBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016136687&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Hall, Barry G. 1942- Phylogenetic trees made easy a how-to manual Datenverarbeitung Phylogeny Data processing Molekularbiologie (DE-588)4039983-7 gnd Phylogenetische Systematik (DE-588)4174592-9 gnd Phylogenie (DE-588)4076110-1 gnd Phylogenetik (DE-588)4174591-7 gnd Datenverarbeitung (DE-588)4011152-0 gnd |
| subject_GND | (DE-588)4039983-7 (DE-588)4174592-9 (DE-588)4076110-1 (DE-588)4174591-7 (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 Phylogeny Data processing Molekularbiologie (DE-588)4039983-7 gnd Phylogenetische Systematik (DE-588)4174592-9 gnd Phylogenie (DE-588)4076110-1 gnd Phylogenetik (DE-588)4174591-7 gnd Datenverarbeitung (DE-588)4011152-0 gnd |
| topic_facet | Datenverarbeitung Phylogeny Data processing Molekularbiologie Phylogenetische Systematik Phylogenie Phylogenetik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016136687&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT hallbarryg phylogenetictreesmadeeasyahowtomanual |