Bio Phylogenomics

Build marker gene alignments and phylogenetic trees.

Instructions

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