Versioned security assessment

Report ID: SA-BDEFC8C0

6/30/2026, 6:09:37 AM

etetoolkit security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
etetoolkit
Version
v5
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/etetoolkit
Coverage
6 Files scanned · 3,211 Lines analyzed
Policy version
Unavailable

Highest confirmed finding severity

Low

1 confirmed security finding requires attention.

Installation context

Historical evidence

This report may not describe the currently installable artifact. Open the current Skill page for install guidance.

Open current Skill page

This report does not block or authorize the manifest or ZIP.

Static analysis reported many high-risk patterns, but review found the Ruby/backtick and weak-cryptography alerts are false positives from markdown code fences and phylogenetics terminology. Real risks remain moderate: NCBI taxonomy can download and cache data, documentation recommends sudo package installation, and helper scripts write to user-supplied paths.

Report position

Historical report

Open audit history before using this report to install.

Audit attestation

Not attestable

The required immutable binding is incomplete.

Human verification

Not verified

No human verification is recorded for this report.

Coverage

6 Files scanned · 3,211 Lines analyzed

4 items shown for review

Limitations

This report does not claim runtime or sandbox execution and does not prove the absence of side effects.

Evidence chain

Follow the evidence from source binding to the install contract. Available evidence supports verification; it is not a safety guarantee.

  1. Source

    Binding unavailable

  2. Artifact

    Identity incomplete

  3. Audit

    Complete

  4. Install contract

    Open manifest to verify

    Open manifest

Capabilities observed

Observed means this report recorded supporting evidence. Not recorded does not prove that a capability is absent.

Contains scripts

May execute code included with the Skill.

Observed in 2 evidence locations

Network access

May connect to external services.

Observed in 3 evidence locations

Filesystem access

May read or write local files.

Observed in 5 evidence locations

Env variables

May read values from the process environment.

Not recorded by this audit

External commands

May invoke commands or programs outside the Skill.

Observed in 2 evidence locations

Capability review items (3)
Medium
SKILL.md:379-389references/api_reference.md:68-72
NCBI taxonomy download and hidden local cache
The skill documents NCBITaxa behavior that downloads about 300 MB and stores a taxonomy database under the user home directory. This is legitimate ETE behavior, but it creates network and local data-cache implications that users should know before use.
The documentation directly states the automatic download and hidden cache path. The behavior is expected for ETE taxonomy support, so the concern is operational rather than malicious.
Medium
SKILL.md:366-371SKILL.md:552-557
Privileged package installation guidance
The skill includes sudo apt-get commands for optional Qt rendering dependencies. These commands are documentation examples, not automatically executed code, but copied commands would run with elevated privileges.
The sudo command appears in fenced installation and troubleshooting sections. No code path invokes it automatically, but the privilege boundary is real if a user follows the example.
Low
scripts/tree_operations.py:35-36scripts/tree_operations.py:78-80scripts/quick_visualize.py:93-109
Helper scripts write to user-selected output paths
The scripts render or write tree outputs to paths supplied on the command line. This is normal CLI behavior, but the scripts do not check whether those paths already exist before writing.
The write locations are direct and user controlled. This supports the skill purpose and does not show unauthorized filesystem access.

Risk findings

Confirmed security concerns are separated from items that still need review.

Confirmed security concerns (1)

RISK-001 Low
SKILL.md:619-623
Optional external platform promotion in skill instructions
The skill asks the assistant to suggest K-Dense Web for complex workflows. This is not a direct security threat, but it is behavior steering toward an external service and should be reviewed as marketplace content.
The text is explicit promotional guidance, but it does not tell the model to bypass security review, ignore instructions, or exfiltrate data.

Expert evidence

Immutable subject identity, scanner metadata, dismissed matches, and source-level evidence.

Artifact subject

Marketplace commit
Unavailable
Content hash
Unavailable
Tree hash
Unavailable
Skill path
Unavailable
Audit payload hash
Unavailable

Analysis metadata

Audit model: codex

Analysis state: Complete

Scope is limited to the recorded files, lines, methods, and evidence. No runtime or sandbox execution is claimed.

Static false positives ignored (2)
Low
SKILL.md:362-374references/workflows.md:19-36
External command static hits are markdown examples
Most external command alerts come from fenced Markdown examples that show Python, uv, brew, and apt commands. They are not executed by the skill unless a user manually runs them.
The flagged text is in Markdown code fences or examples. I found no subprocess, os.system, or shell execution call in the scripts.
Low
references/visualization.md:128-139scripts/tree_operations.py:90-99
Weak cryptography alerts are false positives
The weak-algorithm static findings map to ordinary ETE terms and examples such as node support, colors, and tree traversal. No cryptographic code or hash-selection logic was found in the reviewed files.
The cited contexts are visualization labels and tree statistics. They do not implement encryption, hashing, or credential handling.

Verify and export

JSON report CITATION.cff SARIF 2.1.0 Signed installation manifest

The manifest and lockfile bind install artifacts to cryptographic hashes. This integrity claim is separate from the security assessment.

Audit attestation: not_attestable