Phylogenetic Tree Construction¶

Phylogenetic diversity metrics (Faith's PD, UniFrac) require a rooted phylogenetic tree. We use SEPP (SATe-enabled Phylogenetic Placement) to insert our ASVs into the GreenGenes2 reference backbone tree, which is more accurate than building a de novo tree from our sequences alone.

Runtime

The SEPP placement step takes approximately 1.5 hours with 4 threads. During the workshop we copy a pre-built tree instead. Run SEPP on your own data after the workshop.

Get the SEPP Reference Database¶

cp /pl/active/courses/2025_summer/CSU_2025/q2_workshop_final/QIIME2/2022.10.backbone.sepp-reference.qza .

Run SEPP (Optional, ~1.5 hours)¶

Place your ASVs onto the reference tree:

qiime fragment-insertion sepp \
  --i-representative-sequences seqs.qza \
  --i-reference-database 2022.10.backbone.sepp-reference.qza \
  --o-tree tree_gg2.qza \
  --o-placements tree_gg2_placements.qza \
  --p-threads 4

Get the Pre-Built Tree (Workshop Shortcut)¶

For the workshop, copy the tree that was already built from this dataset:

cp /pl/active/courses/2025_summer/CSU_2025/q2_workshop_final/QIIME2/tree_gg2.qza .

Dataset Specificity

This pre-built tree was constructed specifically from the ASVs in this workshop dataset. Do not use it for your own data, you must run SEPP or another tree-building method on each new dataset.

Outputs¶

File	Type	Description
`tree_gg2.qza`	Artifact	Rooted phylogenetic tree with ASVs placed
`tree_gg2_placements.qza`	Artifact	Detailed placement information (from SEPP)

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