Originally, MAFFT is a multiple sequence alignment program for unixUNIX-like operating systems. However, currently, it is available for Mac OS XmacOS, Linux, and Windows. It is used for both nucleotide and protein sequences.
MAFFT home pagehomepage: http://mafft.cbrc.jp/alignment/software
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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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Offset (works like gap extension penalty) — offset value, which works like the gap extension penalty, for group-to-group alignment.
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