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vsearch cluster-features-closed-reference) poduces an ‘clustered-sequences’ artifact where the original sequence ID has been replaced by the sequence ID of the reference sequences (e.g. from silva_132_97_16S.fna) .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!