Originally, 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.
MAFFT home page: http://mafft.cbrc.jp/alignment/software
To make MAFFT available from UGENE:
Install the MAFFT program on your system.
For example, on Windows you need to specify the path to the mafft.bat file.
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:
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 gap extension penalty, for group-to-group alignment.
Maximum number of iterative refine — specifies the number of cycles of iterative refinement to perform.