I’m interested in finding closely related species for a group of ASVs (classified as Aliivibrio) in a reference database, what’s the best way to proceed? I know that a better way to answer the question is to sequence the full-length 16S rRNA gene or whole-genome. But I want to have a look at my 16S data first.
What I can think of:
Check the insertion tree generated from the fragment insertion (SEPP) in iTOL.
However, the taxonomy.qza file generated by the qiime2-feature-classifier is not compatible with the insertion tree.
Build a de novo tree.
Download Aliivibrio reference sequences. Which reference database should I use? I used SILVA 132 Ref NR database for the taxonomic classification. Maybe I should use SILVA 132 Ref?
Extract amplicon sequences from the Aliivibrio reference sequences using the universal primers.
Build a de novo tree using fastree, raxml or iqtree.
Ideally, the de novo tree can should be built using command line tools only.
Any suggestions or comments are greatly appreciated!