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mega4

mega4

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Published by: fdlab on Apr 08, 2014
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MEGA
Molecular Evolutionary Genetics Analysis
VERSION 4
Koichiro Tamura, Joel Dudley Masatoshi Nei, Sudhir Kumar
Center of Evolutionary Functional Genomics Biodesign Institute  Arizona State University
 
 i
1
 
Table of Contents
2
PREFACE.......................................................................................................1
 
Copyright.................................................................................................................1
 
Guide to Notations Used.........................................................................................2
 
Preface....................................................................................................................3
 
 Acknowledgements.................................................................................................5
 
MEGA Software Development Team......................................................................6
 
Citing MEGA in Publications...................................................................................7
 
3
PART I: GETTING STARTED........................................................................9
 
Installing MEGA.......................................................................................................9
 
System Requirements....................................................................................................9
 
Installing MEGA..............................................................................................................9
 
Uninstalling MEGA.........................................................................................................9
 
Features & Support...............................................................................................10
 
Feature List...................................................................................................................10
 
Using MEGA in the Classroom.....................................................................................22
 
Technical Support and Updates...................................................................................22
 
Reporting Bugs.............................................................................................................22
 
Guide to Notations Used..............................................................................................22
 
 A Walk Through MEGA.........................................................................................23
 
Introduction to Walk through MEGA.............................................................................23
 
Creating Multiple Sequence Alignments......................................................................24
 
 
 
Tests of the Reliability of a Tree Obtained...................................................................28
 
Working With Genes and Domains..............................................................................29
 
Test of Positive Selection.............................................................................................30
 
Managing Taxa with Groups........................................................................................31
 
 
Constructing Trees from Distance Data.......................................................................33
 
4
PART II: ASSEMBLING DATA FOR ANALYSIS.........................................35
 
Text File Editor and Format Converter..................................................................35
 
Trace Data File Viewer/Editor...............................................................................37
 
Web Browser & Data Miner ...................................................................................38
 
Some Text Editor Utilities......................................................................................39
 
Open Saved Alignment Session...................................................................................39
 
Copy Screenshot to Clipboard.....................................................................................39
 
Format Selected Sequence..........................................................................................40
 
Reverse Complement...................................................................................................40
 
Convert to Mega Format (in Text Editor)......................................................................40
 
Building Sequence Alignments..............................................................................40
 
 Alignment Explorer.......................................................................................................40
 
Creating Multiple Sequence Alignments......................................................................41
 
 Aligning coding sequences via protein sequences......................................................42
 
CLUSTALW..................................................................................................................43
 
BLAST..........................................................................................................................45
 
Menu Items in the Alignment Explorer.........................................................................47
 
5
 

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