qiime2 equivalent of the align.seqs function in mothur

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Hello,
I have checked q2 alignement [alignment — QIIME 2 2020.2.0 documentation] and to my understanding you cannot align seqences against an aligned database (like silva in our case).

Then I found out a community tutorial: Q2-alignment: reference based alignment using SINA but SINA seems not available in qiime2 :frowning:

Then I found a very interesting topic:Alignment on Reference Database and the user turboqiimer has exactly the same request.

According the above mentioned topic it seems like MAFFT now supports ref based alignments, but those features are not available in the Qiime 2 plugin yet.

I was wondering the following:

  • Any idea by when SINA will be available in qiime 2
  • Aliternatively does anyone has tested MAFFT (independently of qiime2) to align fasta files on aligned reference database (silva)?

Thanks a lot

Francis