Recent updates to the NCBI BLAST web page are not compatible with the integrated web browser used in MEGA7, MEGA6, and MEGA5. Because these versions are no longer actively developed the issue will not be fixed. The workaround is to either install MEGA X or use NCBI BLAST from your own browser (e.g. Chrome, Firefox, Edge, Windows Explorer, Safari, etc...). When using BLAST from your own browser, you can download the results in the FASTA format and then open the downloaded file in MEGA's Alignment Explorer.
The PDF export option in MEGA's Tree Explorer is a work in progress and is not feature complete. Consequently, italic and bold font styles are not preserved when exporting trees to PDF files.
As of macOS version 10.15 (Catalina), Apple has dropped support for 32-bit applications entirely. To run MEGA7 on Catalina and later versions of macOS, the Windows version of MEGA7 can be used if it is ran using virtualization software such as VMWareFusion. MEGAX will run on Catalina and later starting in version 10.1.4.
Microsoft Windows has a setting to "Change the size of text or other items on your screen" which when not set to the default value (100%) breaks the mapping of mouse clicks in the Tree Explorer window. The workaround is to set this option to the default value.
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 .
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:
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.
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.
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 .
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)
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.