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: When to Use This Skill Use phylogenetics when: - Evolutionary relationships : Which organism/gene is most closely rela…