alterlab-phylogenetics

# 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. ```bash # 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 # Python visualization layer uv pip install "ete3==3.1.3" # also needs numpy<2 and PyQt5 for rendering ``` > ETE3 (3.1.3) is the last ete3 release and can be fragile to install on Python ≥3.12 (pins old numpy/PyQt5). If `t.render()` fails, fall back to writing the Newick tree and viewing it in FigTree/iTOL, or use the maintained successor `ete4` (note: ete4 changed the `TreeStyle`/`render` API, so the snippets below are ete3-specific). ## When to Use This Skill Use phylogen...