phylogenetics
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.
npx skills add LeonChaoX/qinyan-academic-skills --skill phylogenetics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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**:
- Overview
- When to Use This Skill
- Standard Workflow
- 1. Multiple Sequence Alignment with MAFFT
- 2. Trim Alignment (Optional but Recommended)
- 3. IQ-TREE 2 — Maximum Likelihood Tree
- 4. FastTree — Fast Approximate ML
- 5. Tree Analysis and Visualization with ETE3
- 6. Complete Analysis Script
- IQ-TREE Model Guide
- DNA Models
- Protein Models
- Best Practices
- Additional Resources
Conda (recommended for CLI tools) conda install -c bioconda mafft iqtree fasttree pip install ete3
What does the phylogenetics skill do?
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.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill phylogenetics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.