MOLECULAR EVOLUTIONARY
GENETICS ANALYSIS
Authors: Koichiro Tamura, Glen Stecher, Daniel Peterson, and Sudhir Kumar
Version 6.0.5
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Frequently Asked Questions

Q1a. Do I need to purchase a license to use MEGA?

No. MEGA is provided free of charge for all research and educational purposes. However, it is not permissible to redistribute MEGA in any form to other users. We require that all users download their own copy of MEGA from our website directly. MEGA is protected by all applicable copyright laws.

Q1b. Can I install MEGA in a classroom/lab using a script?

Because MEGA includes many statistical methods for the study of molecular evolution in an interactive framework, it is instructive for classroom teaching. If you are interested in using MEGA in the classroom/lab, there are no restrictions. Your students may download a copy from the website www.megasoftware.net or you may install copies on multiple computers in a common computing area. However, if you want to use MEGA in any other form, please contact the authors by e-mail (s.kumar@asu.edu).

If you are using MEGA in classroom teaching, please send us the following information by e-mail for our records (s.kumar@asu.edu). (1) Your name, position and institution, (2) course number and title, (3) number of students, and (4) course semester and year.

Q2. I am not a member of an educational institution. May I still use MEGA?

Yes, MEGA is provided free of charge for commercial institutions as well. However, it is not permissible to redistribute MEGA in any form to other users. We require that all users download their own copy of MEGA from our website directly. MEGA is protected by all applicable copyright laws.

Q3. How do I cite MEGA?

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

Q4. I have an idea on how to improve MEGA. How can I contact the authors?

The authors of MEGA appreciate all forms of user suggestions and feedback. In order to properly address each suggestion, we encourage the use of the Suggestion Box form found in the Support/Feedback section of the MEGA website.

Q5. I discovered a software bug in MEGA. What should I do?

Please report the bug to the MEGA development team immediately using the Bug Report submission form on the MEGA website. User-submitted bug reports are invaluable to the MEGA development team. Due to limited resources, you may not receive a reply to your bug report immediately, but we can assure you that each bug report will be addressed and responded to as soon as possible by a member of the MEGA development team.

Q6. What if I use MacOSX?

As of MEGA 5.1, MacOSX Snow Leopard is supported; simply download the .dmg file and install like normal. MacOSX systems prior to MacOSX Snow Leopard (10.6) are not supported as they are missing certian dependancies.

Q7. What if I use Linux?

We currently do not provide executables for Linux. However, there are many software applications that allow users to run native Windows applications such as MEGA on Linux systems. For example are Wine, VMWare, VirtualBox, and many others.

Q8. What is this X11 program that opens with MEGA on MacOSX?

X11 is a program that comes with MacOSX Leopard and is essential for displaying MEGA on the Mac. If you close X11 MEGA will close as well.

Q9. Is it possible to obtain MEGA on CD-ROM?

Yes. If you are unable to download MEGA from the website, then you should write to the MEGA team to request a CD-ROM distribution of MEGA. Please be sure to include your full name and complete mailing address in your request. Since mail services can be slow, please attempt to download MEGA twice before requesting a CD.

Q10. Can I use MEGA in a shared (Terminal Server) environment?

Yes, In version 4, we have built support for a multi-user environment, which will allow each user of the same computer to keep his/her customized settings, including file locations, window sizes, choice of genetic code table, and previously-used analysis options. This feature will facilitate educational and laboratory usage where a single computer is often shared by multiple users.

Q11. MEGA comes up when I click on the file with extension FAS. How can I disable this?

Simply right-click on the file with the FAS extension to navigate to the properties item. You can then select the program that you wish to associate with that extension.

Q12. How can I use MEGA with the error message "no common sites found for computing distance"?

You must identify which taxon has no common sites with others, and then remove them in order to continue your computing. Please follow this procedure to check the number of common sites between taxa:

1. Click Distances|Compute pairwise from the main menu
2. In the Analysis Preference window, select " L: No. of Valid Common Sites" from drop down for the option "Substitutions to Include"
3. Click "compute" button to get a matrix.

The number in the matrix indicates the number of common sites between sequences that are available for analysis. When this number is zero, there are no common sites. To get around this problem, you may want to eliminate some sequences. In addition, the use of the "Pairwise-Deletion" option for handling alignment gaps and missing data may also be employed.

Q13. Can I use the molecular dating options in MEGA for the Newick format tree with branch lengths?

Yes. MEGA5.0 allows the use of the time tool when the Newick format trees are read-in, as long as they have branch lengths.

Q14. I use MEGA on a network drive. When the network connection is unavailable/broken, why does MEGA display an error message after I try to open a file or close the application?

MEGA can only be used over the network if the directory where MEGA EXE is stored is available for reading (not writing). The user does not need writing privileges on the network. If your bug report indicates that you have an unreliable network connection, then it will be impossible to use MEGA reliably.

MEGA also writes temporary files in the User's Home Directory. This local directory will often be housed on the local computer (in which MEGA EXE is running), and it will always be available. A completely network-based use of MEGA (including User's Home Directory) will cause problems due the non-reliability of network connections (and thus temporary and setup files).

Q15. How do I prevent the "MEGA Update Available" message from showing up ever?

Go to your MEGA appdata directory eg. %appdata%/MEGA5_5XXXXXX\, then /Private/Ini/ and edit the ignore_updates.ini file. Change the 0 to a 1.
If you are running the MEGA exe from a remote computer this should work too.

Q16. I'm converting a file to MEGA format using the built in converter, but get an error message/invalid result/crash. Whats wrong?

Many programs which write out their own files don't stick to the official file format format. This means MEGA has to be able to handle lots of slightly different implementations of the same file format.
We try our best to be able to convert all file formats but including formats which don't exactly match their format.
Check the file you want to convert, and make sure there are NO spaces in the taxa/sequence names as this often can cause issues.

Q17. Why can't I view branch lengths in a bootstrap concensus tree?

MEGA does not compute or provide branch lengths for consensus tree, as they generally contain multi-furcations due to the partition frequency cut-offs. Estimates of branch lengths in these cases are not correct, as the collapsed partitions have non-zero lengths in reality but they are not statistically resolved (i.e., lack of significance by bootstrap method) so they are drawn accordingly on the screen.
Only the branching pattern from the bootstrap tree should be viewed as is, and the branch lengths should be what you see in the "Original Tree" tab.

 

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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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