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Phylogenetics · mkurman | DecimalAI

scienceby mkurman

Phylogenetics

mkurman/phylogenetics

Source mkurman/zorai ↗License MIT

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.

SkillScore71Maintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

Passed 16 of 23 test cases with the skill, and 13 of 23 without it.

Without skill58%

With skill71%

Checks it passed that the model alone missed

Recommends Q.pfam+G4 for Pfam protein families
Recommends GTR+G4 as the most flexible DNA substitution model
Recommends JTT+G4 for the Jones-Taylor-Thornton classical protein model

3 fixed14 passed either way7 still failing0 broke

Pass-rate lift: +13 pp
Tokens: +8%
Agent turns: 0%
Response time: -27%

Model gemini-3.6-flashMeasured 8/21/2026v117 of 24 cases passed with skill · 23 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-phylogenetics/SKILL.md https://app.decimal.ai/s/mkurman-phylogenetics/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-phylogenetics, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-phylogenetics/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-phylogenetics

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-phylogenetics/SKILL.md https://app.decimal.ai/s/mkurman-phylogenetics/SKILL.md

Raw file: /s/mkurman-phylogenetics/SKILL.md ↗ · machine-readable summary at /s/mkurman-phylogenetics.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 2 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 2

Prompt

I am configuring a manual nucleotide substitution model for a highly variable non-coding DNA region where all 6 substitution rates and base frequencies differ. Which nucleotide model represents the most flexible General Time Reversible model with gamma-distributed rate heterogeneity?

What was checked, without and with the skill
Checked	Without skill	With skill
Recommends GTR+G4 as the most flexible DNA substitution model	Missed	Passed

case-09 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md39 lines3 filesincludes scripts

-|-------------|---------| | 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/

Track record

Benchmark

16 / 23

test cases passed, vs 13 / 23 without

Adoption

Users: 1
Times used: 12

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills/phylogenetics/SKILL.md

View on GitHub ↗

License UnknownImported 8/3/2026Version v1Bundled 2 files · scripts

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