Bio Phylogenomics

Build marker gene alignments and phylogenetic trees.

Instructions

Extract marker genes or SSU rRNA sequences.
Align and trim sequences using project-standard workflows.
Build ML trees with bootstraps:
Standard accuracy: Use IQ-TREE (comprehensive model selection, publication-quality)
Fast mode: Use IQ-TREE -fast (exploratory analysis, large datasets >10K sequences)
Very large datasets: Use VeryFastTree (>100K sequences, ultra-fast)
Post-process trees with ETE Toolkit:
Calculate tree statistics (branch lengths, distances, topology metrics)
Root, prune, or collapse nodes as needed
Filter by bootstrap support values
Add taxonomic or trait annotations
Generate publication-quality visualizations

Task	Action
Run workflow	Follow the steps in this skill and capture outputs.
Validate inputs	Confirm required inputs and reference data exist.
Review outputs	Inspect reports and QC gates before proceeding.
Tool docs	See `docs/README.md`.
References	- See ../bio-skills-references.md

Prerequisites:

Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
Marker gene set or alignments available. Inputs:
markers.faa (marker genes) or alignments.fasta

Alignment length and missingness meet project thresholds.
Bootstrap support summary meets project thresholds.
On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
Verify markers.faa is non-empty and aligned sequences are consistent.

markers.faa (marker genes) or alignments.fasta

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.