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MCP server for phylogenetic inference — never returns a topology without its support
The publisher performed an authenticated act of publication — proving control of a namespace in the official MCP registry, or appearing in a first-party catalogue an operator curates. That establishes WHO published it. It is not a security finding, and attested artifacts carry Flagged verdicts too.
1 critical finding reported by cisco-skill-scanner, 0 of them in the installed artifact. The composite score alone does not reflect this — read the per-scanner reports below.
pypi: phylokit-mcp @ 0.4.0, 0 findings
Choose your runtime: the CLI writes the mcpServers config entry for that target.
nerlo install --target claude-code -- phylokit-mcp
Install respects the composite badge: Clean proceeds, Caution prompts for confirmation, and Flagged is refused. Write operations require an API token.
7 of 11 scanners examined this package. The rest do not apply to it — language, ecosystem and packaging decide which analyzers can say anything, and a scanner that cannot examine an artifact reports nothing rather than passing it.
v2.0.11
9 findings · 8.7s
v0.3.26
5 findings · 1.8s
v0.1.0
0 findings · 27.7s
v0.1.0
0 findings · 27.7s
v0.1.0
0 findings · 17.2s
v0.71.0
0 findings · 0.3s
v2.3.8
0 findings · 1.3s
v1.4.0
This scanner found nothing in this artifact that it assesses. What each scanner covers
0 findings · 0.3s
v0.71.0
No container image was published for this artifact. What each scanner covers
0 findings · 0.0s
No report in this scan: capslock, govulncheck.
4 scans on record. Every scan's full results are retained immutably for 24 months.
| Completed | Composite | Change | Scanners | Status |
|---|---|---|---|---|
| Aug 5, 2026 | Flagged92 | — | agentshield ·n/a: not applicablecisco-skill-scanner: completeagent-audit-kit: completenerlo-behavioral: completenerlo-install-instruction: completenerlo-multi-source: completetrivy: completeosv-scanner: completetrivy_image ·n/a: not applicable | completed |
| Aug 3, 2026 | Flagged92 | Clean → Flagged | agentshield ·n/a: not applicablecisco-skill-scanner: completeagent-audit-kit: completenerlo-behavioral: completenerlo-install-instruction: completenerlo-multi-source: completetrivy: completeosv-scanner: completetrivy_image ·n/a: not applicable | completed |
| Aug 2, 2026 | Clean98 | — | agentshield ·n/a: not applicablecisco-skill-scanner: completeagent-audit-kit: completenerlo-behavioral: completenerlo-install-instruction: completenerlo-multi-source: completetrivy: completeosv-scanner: completetrivy_image ·n/a: not applicable | completed |
| Jul 31, 2026 | Clean99 | — | agentshield ·n/a: not applicablecisco-skill-scanner: completeagent-audit-kit: completenerlo-behavioral: completenerlo-install-instruction: completenerlo-multi-source: completetrivy: completeosv-scanner: completetrivy_image ·n/a: not applicable | completed |
Findings in files this artifact installs stand as reported; a model re-read the rest and said which ones it believes are false positives. This is a second opinion published beside the evidence, not a correction to it: the per-scanner reports above are unchanged, every dismissed finding is still listed there at its original severity, and the score and the Flagged badge are computed from those raw severities alone. Nothing below moved them.
Out of 14 findings across every scanner that examined this package. 1 of 1 finding rated critical by their scanner was among the dismissals.
Two keys had to turn. The model had to name a reason from a fixed list of six, and a deterministic check of ours — over which files this artifact actually installs — had to independently agree. Anything it could not corroborate is in “not reviewed” above, at full severity.
4 Documentation or example — The match is in documentation or sample code, confirmed by our own check to be outside the installed artifact.
Rules: SOCIAL_ENG_VAGUE_DESCRIPTION, MANIFEST_MISSING_LICENSE · Files: /repo/docs/SKILL.md, /repo/.github/SKILL.md · reported by cisco-skill-scanner
1 CI or editor configuration — The match is in build, CI or editor configuration, confirmed by our own check to be outside the installed artifact.
Rules: MANIFEST_INVALID_NAME · Files: /repo/.github/SKILL.md · reported by cisco-skill-scanner
1 Test or fixture file — The match is in a test or fixture. Our own check confirmed the file is not part of what gets installed.
Rules: YARA_command_injection_generic · Files: /repo/tests/server.schema.json · reported by cisco-skill-scanner
These findings are in files this artifact installs and are not placeholder values. No false-positive basis can be corroborated for such a finding, so this review never dismisses one; they were not sent to the model and stand at their scanner's severity.
1 AAK-HEALTHCARE-AI-004
Files: CHANGELOG.md · reported by agent-audit-kit
1 AAK-MCP-005
Files: .mcp.json · reported by agent-audit-kit
1 AAK-MCP-007
Files: .mcp.json · reported by agent-audit-kit
1 AAK-OAUTH-3P-001
Files: pyproject.toml · reported by agent-audit-kit
1 AAK-SUPPLY-001
Files: .mcp.json · reported by agent-audit-kit
1 HIDDEN_DATA_FILE
Files: /repo/.zenodo.json · reported by cisco-skill-scanner
1 MANIFEST_MISSING_LICENSE
Artifact includes high-risk external code execution capability.
The artifact contains a high-severity finding related to external code execution within `.mcp.json`. It also includes medium-severity findings for third-party OAuth integration, which may involve credential access, and other medium-severity issues. A low-severity finding indicates the presence of a hidden data file.
Concern level assessed by the review: High. This is the review's scale, not the registry badge.
Reviewed by gemini-2.5-flash. The model sees the findings, not your code, and cannot change a score.
Files: /repo/SKILL.md · reported by cisco-skill-scanner
1 SOCIAL_ENG_VAGUE_DESCRIPTION
Files: /repo/SKILL.md · reported by cisco-skill-scanner