Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral ph…
---
name: phylogenetics
description: Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
license: Unknown
metadata: {"version": "1.0", "skill-author": "Kuan-lin Huang"}
---
# 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
```
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