Phylogenetics
Overview
Phylogenetic analysis reconstructs the evolutionary history of biological sequences (genes, proteins, genomes) by inferring the branching pattern of descent. This skill covers the standard pipeline:
- MAFFT — Multiple sequence alignment
- IQ-TREE 2 — Maximum likelihood tree inference with model selection
- FastTree — Fast approximate maximum likelihood (for large datasets)
- ETE3 — Python library for tree manipulation and visualization
Installation:
# Conda (recommended for CLI tools)
conda install -c bioconda mafft iqtree fasttree
uv pip install ete3
# ete3's TreeStyle/NodeStyle rendering lives in its Qt backend, so image output
# needs PyQt5 as well; tree parsing and statistics work without it.
uv pip install PyQt5
When to Use This Skill
Use phylogenetics when:
- Evolutionary relationships: Which organism/gene is most closely related to my sequence?
- Viral phylodynamics: Trace outbreak spread and estimate transmission dates
- Protein family analysis: Infer evolutionary relationships within a gene family
- Horizontal gene transfer detection: Identify genes with discordant species/gene trees…
