Prerequisites: This skill requires uv. See the README for installation instructions.

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