QIIME 2 2017.9 now runs only non-phylogenetic metrics when executing core-metrics (which is pertinent to ITS analyses). To include phylogenetic metrics you can run core-metrics-phylogenetic! Check out the release announcement to learn more! 
QIIME 2 2017.9 now runs only non-phylogenetic metrics when executing core-metrics (which is pertinent to ITS analyses). To include phylogenetic metrics you can run core-metrics-phylogenetic! Check out the release announcement to learn more!