MOLECULAR EVOLUTIONARY
GENETICS ANALYSIS
Authors: Koichiro Tamura, Glen Stecher, Daniel Peterson, and Sudhir Kumar
Version 6.0.5
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Known Issues

Integrated help system has problems for the Mac version

When utilizing the integrated help for the Mac version of MEGA, the Index and Search tabs may be inoperable. The workaround is to use the online help manual.

PDF images are sometimes cropped

Some users have experienced a problem where saving tree images to a pdf file results in a cropped image. This is a mysterious bug that we have never been able to reproduce. There are a couple workarounds:

  • Save the image as a png or emf file.
  • Copy the image to the system clipboard and paste the image into GIMP, Photoshop, or other image editing application. Then save the file in the desired format. ***Note*** GIMP might complain that there is no data on the clipboard. If so, first paste the image into a Word file, copy it from the Word file and then paste into GIMP.

Starting in MEGA 6, older tree session files cannot be opened and alignment session files lose some information

A much needed design change in MEGA's session file system has made it necessary in MEGA 6 to disallow opening of tree session files that were generated using previous version of MEGA. A workaround is to open an older session file using the version that was used to generate it (older versions can be downloaded here), export the tree to a .nwk file, then open the .nwk file in MEGA 6. A new session can then be saved.

Additionally, when opening alignment session files that were created with previous versions of MEGA, some information is lost. The sequence data will be retrieved but the settings used for alignment as well as the form state (font, colors, etc...) will be lost.

Tree session files (.MTS) generated with MEGA 5.05 and earlier have trouble being viewed in MEGA 5.1 and MEGA 5.2

If you have files generated with MEGA 5.05 or earlier, they are best viewed in MEGA 5.05. You may download MEGA 5.05 here.

MEGA for Mac Stability

Most Mac users have reported positive experiences when using MEGA (using the Wineskin wrapper and installer that we provide). However, we also have recieved feedback from some Mac users that have experienced stability issues.
If you are one of the Mac users who experiences problems with the wrapper that we provide, there are alternative options for running MEGA on a Mac system. For instance, MEGA can be run using virtualization or emulation software. Many options for doing so are available including Parallels(commercial), Crossover(commercial), VMWareFusion(commercial) or VirtualBox(free)

MEGA Compatiblity with WINE (Wine Is Not an Emulator) Project

Several users have written into us saying that MEGA runs ok under WINE on Linux systems. We do not offer support for users running MEGA on WINE, and can not offer assistance on installing or configuring WINE.

 

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Resources

Book Book Molecular Evolution and Phylogenetics (2000)
Introductory book containing many examples for use with MEGA.
Book Book Phylogenetic Trees Made Easy (2011) (2007)
A cookbook for learning phylogenetic analysis using MEGA and other programs.
  MEGA: Molecular Evolutionary Genetics Analysis (1993).
Institute of Molecular Evolutionary Genetics. University Park, PA, USA.
  Building Phylogenetic Trees from Molecular Data with MEGA(2013)
A Paper, which explains how to construct phylogenetic trees using MEGA.
  A Walk Through MEGA
Step-by-step instructions to learn how to use MEGA.
  Useful Publications
MEGA related publications.
  MEGA Team
Research and development team.
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Using MEGA

  NEW! Online Manual NEW!
Reference and documentation.
  MEGA 6 release notes
A list of major changes and new features in the current stable version of MEGA.
  Update History
A comprehensive list of major changes with each software release.
  Report a Bug
Help us improve our software by reporting problems you encounter using MEGA.
  Example Data
The following data files are provided as downloads for reference purposes.
  Suggestion Box
User feedback plays an important role in the development of MEGA.
  FAQ
Frequently asked questions.
  Known Issues
Known issues which exist in MEGA.
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Download Stats

MEGA 6 Downloads:
MEGA 5 Downloads:
MEGA 4 Downloads:
MEGA 3 Downloads: 106,285
MEGA 2 Downloads: 69,828
MEGA 1 Downloads: 2,929
Contact Us
Email us with any questions or concerns.
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Citing MEGA in a Publication

Citation for MEGA 6:
Tamura K, Stecher G, Peterson D, Filipski A, and Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution 30: 2725-2729.
- Download PDF

Citation for MEGA-CC:
Kumar S, Stecher G, Peterson D, and Tamura K (2012) MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis. Bioinformatics 28:2685-2686.
- Download PDF

Citation for MEGA 5:
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
- Download PDF

Citation for MEGA 4:
Tamura K, Dudley J, Nei M and Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
- Download PDF

Citation for MEGA 3:
Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. Briefings in Bioinformatics 5:150-163.
- Download PDF

Citation for MEGA 2:
Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular Evolutionary Genetics Analysis Software. Bioinformatics 17:1244-1245.
- Download PDF

Citation for MEGA 1:
Kumar S, Tamura K, Nei M. (1994) MEGA: Molecular Evolutionary Genetics Analysis Software for Microcomputers. Computer Applications in Biosciences 10:189-191.
- Download PDF

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