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:** ```bash # Conda (recommended for CLI tools) conda install -c bioconda mafft iqtree fasttree pip install ete3 ``` ## When to Use This Skill Use phylogenetics when: - **Evolutionary relationships**: Which organism/gene is most closely related to my sequence? - **Viral phylodynamics**: Trace outbreak spread and estimate transmission dates - **Protein family analysis**: Infer evolutionary relationships within a gene family - **Horizontal gene transfer detection**: Identify genes with discordant species/gene trees - **Ancestral sequence reconstruction**: Infer ancestral protein sequences - **Molecular clock analysis**: Estimate divergence dates using temporal sampling - **GWAS companion**: Place variants in evolutionary context (e.g., SARS-CoV-2 variants) - **Microbiology**: Species phylogeny from 16S rRNA or core genome phylogeny ## Standard Workflow ### 1. Multiple Sequence Alignment with MAFFT ```python import subprocess import os def run_mafft(input_fasta: str, output_f...