How do I install the Phylogenetics skill?

Run npx skillmds@latest add mkurman/phylogenetics in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Is Phylogenetics free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under Unknown.

Who published Phylogenetics?

mkurman (@mkurman) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Phylogenetics by mkurman — Agent Skill

Name: Phylogenetics
Author: mkurman

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.

mkurman 299355e 3 files · 16.3 KB Updated Sep 17, 2026

File contents

-|-------------|---------| | GTR+G4 | General Time Reversible + Gamma | Most flexible DNA model | | HKY+G4 | Hasegawa-Kishino-Yano + Gamma | Two-rate model (common) | | TrN+G4 | Tamura-Nei | Unequal transitions | | JC | Jukes-Cantor | Simplest; all rates equal |

Protein Models

Model	Description	Use case
`LG+G4`	Le-Gascuel + Gamma	Best average protein model
`WAG+G4`	Whelan-Goldman	Widely used
`JTT+G4`	Jones-Taylor-Thornton	Classical model
`Q.pfam+G4`	pfam-trained	For Pfam-like protein families
`Q.bird+G4`	Bird-specific	Vertebrate proteins

Tip: Use -m TEST to let IQ-TREE automatically select the best model.

Best Practices

Alignment quality first: Poor alignment → unreliable trees; check alignment manually
Use linsi for small (<200 seq), fftns or auto for large alignments
Model selection: Always use -m TEST for IQ-TREE unless you have a specific reason
Bootstrap: Use ≥1000 ultrafast bootstraps (-B 1000) for branch support
Root the tree: Unrooted trees can be misleading; use outgroup or midpoint rooting
FastTree for >5000 sequences: IQ-TREE becomes slow; FastTree is 10–100× faster
Trim long alignments: TrimAl removes unreliable columns; improves tree accuracy
Check for recombination in viral/bacterial sequences before building trees (RDP4, GARD)

Additional Resources

MAFFT: https://mafft.cbrc.jp/alignment/software/
IQ-TREE 2: http://www.iqtree.org/ | Tutorial: https://www.iqtree.org/workshop/molevol2022
FastTree: http://www.microbesonline.org/fasttree/
ETE3: http://etetoolkit.org/
FigTree (GUI visualization): https://tree.bio.ed.ac.uk/software/figtree/
iTOL (web visualization): https://itol.embl.de/
MUSCLE (alternative aligner): https://www.drive5.com/muscle/
TrimAl (alignment trimming): https://vicfero.github.io/trimal/

---name: phylogeneticsdescription: 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----|-------------|---------|| `GTR+G4` | General Time Reversible + Gamma | Most flexible DNA model || `HKY+G4` | Hasegawa-Kishino-Yano + Gamma | Two-rate model (common) || `TrN+G4` | Tamura-Nei | Unequal transitions || `JC` | Jukes-Cantor | Simplest; all rates equal |### Protein Models| Model | Description | Use case ||-------|-------------|---------|| `LG+G4` | Le-Gascuel + Gamma | Best average protein model || `WAG+G4` | Whelan-Goldman | Widely used || `JTT+G4` | Jones-Taylor-Thornton | Classical model || `Q.pfam+G4` | pfam-trained | For Pfam-like protein families || `Q.bird+G4` | Bird-specific | Vertebrate proteins |**Tip:** Use `-m TEST` to let IQ-TREE automatically select the best model.## Best Practices- **Alignment quality first**: Poor alignment → unreliable trees; check alignment manually- **Use `linsi` for small (<200 seq), `fftns` or `auto` for large alignments**- **Model selection**: Always use `-m TEST` for IQ-TREE unless you have a specific reason- **Bootstrap**: Use ≥1000 ultrafast bootstraps (`-B 1000`) for branch support- **Root the tree**: Unrooted trees can be misleading; use outgroup or midpoint rooting- **FastTree for >5000 sequences**: IQ-TREE becomes slow; FastTree is 10–100× faster- **Trim long alignments**: TrimAl removes unreliable columns; improves tree accuracy- **Check for recombination** in viral/bacterial sequences before building trees (`RDP4`, `GARD`)## Additional Resources- **MAFFT**: https://mafft.cbrc.jp/alignment/software/- **IQ-TREE 2**: http://www.iqtree.org/ | Tutorial: https://www.iqtree.org/workshop/molevol2022- **FastTree**: http://www.microbesonline.org/fasttree/- **ETE3**: http://etetoolkit.org/- **FigTree** (GUI visualization): https://tree.bio.ed.ac.uk/software/figtree/- **iTOL** (web visualization): https://itol.embl.de/- **MUSCLE** (alternative aligner): https://www.drive5.com/muscle/- **TrimAl** (alignment trimming): https://vicfero.github.io/trimal/

Frequently asked questions