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 3** — 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 # iqtree is now IQ-TREE 3 # ... 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 # Python visualization layer uv pip install "ete3==3.1.3" # also needs numpy<2 and PyQt5 for rendering ``` > **Binary name:** bioconda's `iqtree` package is now **IQ-TREE 3** (3.1.x) and installs the > executables `iqtree` and `iqtree3` — there is **no `iqtree2`** in it. Call `iqtree`, which > works on both the 2.x and 3.x packages; only reach for a versioned name when two releases > coexist on PATH. IQ-TREE 3 adds MixtureFinder, multi-tree mixture models (MAST), gene/site > concordance fac...