To run the classic MUSCLE use the Align â€£ Align with MUSCLE context menu item in the Alignment Editor.
The dialog contains the list of MUSCLE modes: MUSCLE default, Large alignment, Refine only.
By default UGENE does not rearrange sequence order in an alignment, but the original MUSCLE package does. To enable sequence rearrangement uncheck the Do not re-arrange sequences (-stable) option in the dialog.
One of the improvements to the original MUSCLE package is the ability to align only a part of the model. When the Column range item is selected the region of the specified columns is only passed to the MUSCLE alignment engine. The resulted alignment is inserted into the original one with gaps added or removed on the region boundaries.
To visually select the column range to align, make a selection in the alignment editor first. Then invoke the MUSCLE plugin. Its column range boundary values will automatically match the given selection.