Let me give you an example. I was reading a paper written 'Sequences shorter than 300 nucleotides orlonger than 600 nucleotides were also discarded. The unique se-quences were then aligned in mothur by default setting with referring to the pre-aligned mcr Asequences provided by the Fun-gene Pipeline database'.
I do not need to draw a phylogeny tree. I want only align my sequences with a reference sequences. I found this message in Qiime2 forum:
I am looking for a plugin/action/ method or tool in Qiime2 to align my sequences (query) with reference sequences. By the way, there is an alignemt option in Qiime2, Maff, but its function is de-novo. it does not align the query on the reference sequences.
https://docs.qiime2.org/2019.4/plugins/available/alignment/mafft/
Now, can you help me with this details I gave to you?