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Hi Dil,
MEGA does not handle the MUSCLE alignment on its own, but rather through a separate program. In order to use the MUSCLE alignment, you will need to download the separate MUSCLE application from this website: http://www.drive5.com/muscle/downloads.htm [^] and run the alignment using that. As you'll see there, there is only a 32-bit application available for Windows, and a 64-bit application for Mac OS or Linux. To run the MUSCLE alignment, please refer to the manual located on their website: http://www.drive5.com/muscle/manual/index.html [^] which includes these instructions:
PATH or pathname
The binary file must be in one of the directories specified in your PATH variable, or you must type the full path to the file, e.g. for Linux:
/usr/bin/muscle6.0.98_i86linux32 -in seqs.fa -out seqs.afa
Under the Windows CMD shell, path names are separated by backslashes, e.g.:
C:\MyPrograms\muscle6.2.98_win32.exe -in seqs.fa -out seqs.afa
Run muscle from a shell
muscle will not work if you try to start it in a graphical interface like Windows Explorer or the Mac Finder. You must start it from a command window or shell.
Please let me know if you have any questions.
Christina |
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