Originally, MAFFT is MAFFT is a multiple sequence alignment program for unix-like operating systems. However, currently it is available for Mac OS X, Linux and Windows. It is used for both nucleotide and protein sequences.
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Install the MAFFT program on your system.
Set the path to the MAFFT executable on the External tools tab of UGENE Application Settings dialog.
For example, on Windows you need to specify the path to the mafft.bat file.
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