Yes, thank you for providing me with those details.
The method you cited mentions mothur:
unique se-quences were then aligned in mothur
mothur uses a reference msa when building feature, and some Qiime 2 plugins like dada2 do not need a reference at all.
If you want to use SINA, that community tutorial is a good place to start. MAFFT now supports ref based alignments, but those features are not available in the Qiime 2 plugin yet.
I have another question for you, if you are interested in answering.
The only time I do MSA is when want a phylogeny tree for UniFrac distances or graphs. Why do you want to do MSA?
Colin