Thanks for the suggestion!
Actually we thought of integrating usearch. Your request is a good reason to consider it more carefully (https://ugene.unipro.ru/tracker/browse/UGENE-1805).
You might find useful our clustering feature with phylogenetic trees. Just build a tree and switch on the clustering mode.

Ron, if you want to try clustering mode in UGENE, you need to open the tree and the alignment synchronized.

For example, you could open an alignment and run the "Build tree" dialog. If you use the default settings (see the attached screenshot "tree 1.png") then the built tree will be opened synchronized with the alignment.

On the screenshot "tree 2.png" you can see the blue vertical line. Drag and drop the line to the left or to the right, and the sequences of tree's nodes which are on the right side of the line will be grouped into the clusters.

Also, you can open an existing tree but not build the new one (the screenshot "tree 3.png").