Closed reference clustering (qiime vsearch cluster-features-closed-reference) poduces an ‘clustered-sequences’ artifact where the original sequence ID has been replaced by the sequence ID of the reference sequences (e.g. from silva_132_97_16S.fna) . These IDs are maintained in the subsequent chimera filtering step.
Is it possible to use these squences to create phylogenetic trees and to display the tip labels in the trees by any of the taxonomic levels available via the corresponding taxonomy table of the reference sequences?
I would like to produce nexus trees with easily recognizable branches and tips.
Thank you for any suggestions!
Since the representative OTU sequences produced by closed-ref OTU clustering are the closest reference sequences (with the SILVA ref seq ID), I believe you can actually use one of the pre-aligned trees that come in the SILVA release. These will be based on full 16S alignment and other curation may be applied… but in any case it would save you time. You will need to filter the tree to only contain observed sequences, of course, if you are planning to view this tree.
That is not possible in QIIME 2 — but follow this thread to see a duplicate question and solution.
I hope that helps!
Thank you for forwarding me to the related thread.
At the end of this thread, I found the great support off @iletunic at iTOL and how easy it is to drag and drop qimme2 artifacts into iTOL…
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