Bio Phylogenomics

When to use

• Build marker gene alignments and phylogenetic trees.

Prerequisites

• Tools installed via pixi (see pixi.toml).
• Marker gene set or alignments available.

Inputs

• markers.faa (marker genes) or alignments.fasta

Outputs

• results/bio-phylogenomics/alignments/
• results/bio-phylogenomics/trees/
• results/bio-phylogenomics/phylo_report.md
• results/bio-phylogenomics/logs/

Steps

1. Extract marker genes or SSU rRNA sequences.
2. Align and trim sequences using project-standard workflows.
3. 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)
4. 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

QC gates

• 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.

Validation

• Verify markers.faa is non-empty and aligned sequences are consistent.

Tools

• iqtree v3.0.1 (standard mode and -fast mode for rapid inference)
• veryfasttree v4.0+ (ultra-fast tree inference for massive datasets)
• ete3/ete4 (ETE Toolkit for tree processing, statistics, and visualization)

Tool Selection Workflow

Tree Inference

Choose tree inference tool based on dataset size and accuracy requirements:

Dataset Size	Accuracy Required	Recommended Tool
<1K sequences	High (publication)	IQ-TREE standard
<1K sequences	Medium (exploratory)	IQ-TREE -fast
1K-10K sequences	High (publication)	IQ-TREE standard
1K-10K sequences	Medium (exploratory)	IQ-TREE -fast
10K-100K sequences	High	IQ-TREE standard
10K-100K sequences	Medium/Fast	IQ-TREE -fast
>100K sequences	Any	VeryFastTree

Post-Tree Processing

Use ETE Toolkit for all tree post-processing tasks:

• Tree statistics and metrics
• Tree manipulation (rooting, pruning, filtering)
• Taxonomic annotation
• Visualization and figure generation

Paper summaries (2023-2025)

• summaries/ (include example use cases and tool settings used)

Tool documentation

• IQ-TREE - Maximum likelihood phylogenetic inference with model selection
• VeryFastTree - Ultra-fast approximate maximum likelihood trees
• ETE Toolkit - Tree manipulation, statistics, and visualization

References

• See ../bio-skills-references.md