Originally, MAFFT is a multiple sequence alignment program for UNIX-like operating systems. However, currently, it is available for macOS, Linux, and Windows. It is used for both nucleotide and protein sequences.

MAFFT homepage: http://mafft.cbrc.jp/alignment/software

To make MAFFT available from UGENE:

To use MAFFT open a multiple sequence alignment file and select the Align with MAFFT item in the context menu or in the Actions main menu. The following dialog appears:

     <img src="/wiki/download/attachments/19759722/MAFFT.bmp"/>

The following parameters are available:

Gap opening penalty — Gap opening penalty at group-to-group alignment.

Offset (works like gap extension penalty) — offset value, which works like the gap extension penalty, for group-to-group alignment.

Maximum number of iterative refine — specifies the number of cycles of iterative refinement to perform.