Please see this Galaxy Training Network (GTN) tutorial for help using Unique.seqs in combination with the other Mothur tools: https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
The tool requires a fasta input and the name/count input is optional. Please see the tool form for the exact outputs produced. This includes a new "names" output for downstream use (as needed) - or just run the tool on your fasta dataset and review.
All Galaxy tutorials: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team