Step 5: Generate a tree for phylogenetic diversity analyses - shenjean/diversity GitHub Wiki

Build a phylogenetic tree using fasttree and mafft alignment

qiime phylogeny align-to-tree-mafft-fasttree --i-sequences pe.repseqs.qza --o-alignment pe.aligned.qza \
--o-masked-alignment pe.masked.qza --o-tree unrooted-tree.qza --o-rooted-tree rooted-tree.qza

Phylogenetic placement with SEPP

• Examples: https://library.qiime2.org/plugins/q2-fragment-insertion/16/
• Paper: https://doi.org/10.1128/mSystems.00021-18

Download SEPP reference database

For the reference database, you can download and use SILVA 128 reference database or Greengenes 13_8 SEPP reference database under the “SEPP reference database” section at the bottom of https://docs.qiime2.org/2024.10/data-resources/.

SILVA:

wget https://data.qiime2.org/classifiers/sepp-ref-dbs/sepp-refs-silva-128.qza

qiime fragment-insertion sepp --p-threads 20 \
  --i-representative-sequences pe.repseqs.qza \
  --i-reference-database sepp-refs-silva-128.qza \
  --o-tree insertion-tree.qza \
  --o-placements insertion-placements.qza

Greengenes:

wget https://data.qiime2.org/classifiers/sepp-ref-dbs/sepp-refs-gg-13-8.qza

qiime fragment-insertion sepp --p-threads 20 \
  --i-representative-sequences pe.repseqs.qza \
  --i-reference-database sepp-refs-gg-13-8.qza \
  --o-tree insertion-tree.qza \
  --o-placements insertion-placements.qza

qiime fragment-insertion filter-features \
  --i-table pe.dada2.qza \
  --i-tree insertion-tree.qza \
  --o-filtered-table filtered_table.qza \
  --o-removed-table removed_table.qza