Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Molecular Biology and Evolution.
(to be submitted)
Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.
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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.
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Frequently Asked Questions

Q1. 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.

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?

Please cite MEGA in the following way:

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.

A manuscript describing MEGA 5 is being submitted, once MEGA 5 is released from the Beta testing phase (very early 2011) please cite MEGA in the following way:

Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Molecular Biology and Evolution (to be submitted).

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. 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.

Q7. Can I use MEGA in a shared (Terminal Server) environment?

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.

Q8. 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.

Q9. 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.

Q10. Can I use the molecular dating options in MEGA for the Newick format tree with branch lengths?

Yes. MEGA4 allows the use of the time tool when the Newick format trees are read-in, as long as they have branch lengths.

Q11. 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).

Q12. How can I ignore the current update available message in MEGAs main window?

By clicking the blue [X] link next to "MEGA Update Available" you will ignore the current new version but be notified of subsequent updates.

Q13. 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 works also.