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:

1. MAFFT — Multiple sequence alignment
2. IQ-TREE 2 — Maximum likelihood tree inference with model selection
3. FastTree — Fast approximate maximum likelihood (for large datasets)
4. 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