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: The aligners and tree builders are compiled CLI tools (not on PyPI). Install the binaries via bioconda or Homebrew; install the Python visualization layer with uv.

# CLI binaries — bioconda (cross-platform) ...
conda install -c bioconda mafft iqtree fasttree trimal
# ... or Homebrew on macOS (Apple Silicon): IQ-TREE/TrimAl live in the brewsci/bio tap
brew install mafft fasttree
brew tap brewsci/bio && brew install brewsci/bio/iqtree brewsci/bio/trimal  # iqtree formula ships the iqtree2 binary