5. phylogenetic_diversity.sh

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences rep-seqs.qza \
  --o-alignment aligned-rep-seqs.qza \
  --o-masked-alignment masked-aligned-rep-seqs.qza \
  --o-tree unrooted-tree.qza \
  --o-rooted-tree rooted-tree.qza
  
  
  
  # 1. aligned-rep-seqs.qza
  # 2. masked-aligned-rep-seqs.qza
  # 3. rooted-tree.qza
  # 4. unrooted-tree.qza