@Nicholas_Bokulich thanks a lot.
From my workflow up to the classification and plotting, what intermediate file would I use as input to MAFFT in order to work on getting a rooted tree?
-steffen
Thanks for asking, @steff1088! In general this would be the same exact sequences file that you use as input for taxonomy classification, e.g., could be as simple as the rep-seqs.qza output from cluster-features-open-reference. However, in your case (since you apply an abundance filter to the feature table and then remove these features from the sequences file) you could use the filtered sequences.
I hope that helps!
Wonderful, thanks for this advice as well.
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