phylogenetics
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
Independent static run, no language model, over the same files as the Cisco scan above. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.
- Package
- 3 files, 29 KB
- SKILL.md
- 1093 words, 12+ sections
- Code
- Python (1)
- License
- Unknown
- Compatibility
- Requires MAFFT and IQ-TREE 3 or FastTree executables. Optional tree summaries use Python 3.12 and ete3 3.1.3; rendering also needs PyQt5. Optional trimming needs trimAl. Network access is required for installation, not local inference.
SKILL.md covers: Phylogenetics · When to use · Versions and installation · Optional rendering backend; it can require a working Qt platform plugin. · Workflow · 1. Establish the biological input · 2. Align and inspect · L-INS-i: locally alignable homologs, typically small datasets. · E-INS-i: homologs with large internal gaps. · FFT-NS-i (two refinement cycles), then FFT-NS-2 (progressive). · 3. Infer a tree · Use a reviewed alignment (including any explicit trimming) without realigning.
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 9.2 KB |
references/iqtree_inference.md | doc | 7.2 KB |
scripts/phylogenetic_analysis.py | script | 13 KB |
External hosts referenced
iqtree.github.io etetoolkit.org github.com mafft.cbrc.jp morgannprice.github.io vicfero.github.io
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-phylogenetics-scan.json
- Badge for your README:
- Request a re-scan