{"id":"cmuxiub9y11lyad074e2mw4a7","slug":"etetoolkit","publicId":"1ae296c2-5f56-4738-8bb5-35f5b58d9f66","name":"etetoolkit","description":"Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Applies to existing trees after alignment and phylogenetic inference, rather than inferring trees from raw sequences.","version":"3.0","author":"k-dense-ai","license":"GPL-3.0-or-later","compatibility":"Bundled scripts require Python 3.10+ and ete4 4.4.0 (upstream metadata requires Python >=3.7). Public taxonomy acquisition needs internet access. SmartView uses a local browser/server; static PNG rendering needs ete4[render-sm] and Chrome/Chromium, and Qt PDF/SVG rendering needs ete4[treeview].","status":"completed","overallGrade":"B","scannerVersion":11,"fileCount":9,"hasSkillMd":true,"hasScripts":true,"hasReferences":true,"hasEvals":false,"hasAssets":false,"sourceType":"github","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/etetoolkit","createdAt":"2026-10-07T03:01:51.316Z","completedAt":"2026-10-07T03:01:51.310Z","visibility":"public","publishedAt":"2026-09-10T21:05:41.119Z","category":"","frameworks":[],"badgeStatus":"conditional","downloadCount":0,"verdictRationale":{"summary":"Skill has warnings: 1 warning in security or structure checks.","verdict":"warn","scanners":[{"source":"vettd","weight":1,"verdict":"warn"},{"source":"cisco","weight":0.8,"verdict":"pass"}],"consensus":"warn","warnTriggers":["References external URL — review for indirect prompt injection risk"],"policyVersion":"consensus-v1","hardFailTriggers":[]},"verdictPolicyVersion":"consensus-v1","skillId":"cmtw0o4jbbaptad0774lerhti","findings":[{"id":"cmuxiub9y11lzad07zce5ftbz","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088","owaspLlmCategory":null,"intent":null,"chainId":null,"fingerprint":"42638a8b7e9fc5df27449992eaebc724","filepath":"SKILL.md"}],"scannerRuns":[{"source":"cisco","status":"success","verdict":null,"grade":"A","findingCount":0,"criticalCount":0,"highCount":0},{"source":"vettd","status":"success","verdict":null,"grade":"B","findingCount":1,"criticalCount":0,"highCount":0}],"user":{"name":"Kris Mondlane","image":"https://avatars.githubusercontent.com/u/237055?v=4"},"repository":{"owner":"k-dense-ai","name":"scientific-agent-skills"},"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T19:27:00.568Z","lastVerifiedAt":"2026-10-22T19:27:00.568Z","lastChangeDetectedAt":"2026-10-07T02:47:39.890Z","scannedHash":"b0999ed6213cfd01acb2bbb08b8bc2acff0a6d82","latestUpstreamHash":"b0999ed6213cfd01acb2bbb08b8bc2acff0a6d82","nextCheckDueAt":"2026-10-23T20:31:21.099Z"},"signalCategories":[{"category":"safety","label":"Safety","form":"graded","verdict":null,"rows":[]},{"category":"reliability","label":"Reliability & Quality","form":"graded","verdict":null,"rows":[]},{"category":"performance","label":"Performance","form":"measured","verdict":{"form":"measured","magnitudes":[{"ruleId":"performance/static-context-tokens","label":"Static context tokens","value":3226,"unit":null,"method":"tiktoken/cl100k_base/skill-md-body"}]},"rows":[{"origin":"signal","id":"cmuxiuckg11vcad07yg8oz5s6","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"","relatedId":"","dataCategory":"performance","sourceClass":"scan","source":"vettd","ruleId":"performance/progressive-disclosure","severity":null,"label":"Progressive disclosure","detail":null,"valueNum":null,"valueText":"present","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiubkh11o3ad07sht0xf9s","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"","relatedId":"","dataCategory":"performance","sourceClass":"scan","source":"vettd","ruleId":"performance/static-context-tokens","severity":null,"label":"Static context tokens","detail":null,"valueNum":3226,"valueText":null,"unit":null,"method":"tiktoken/cl100k_base/skill-md-body","derivation":null,"confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null}]},{"category":"cost","label":"Cost","form":"measured","verdict":null,"rows":[]},{"category":"compatibility","label":"Compatibility","form":"unjudged","verdict":{"form":"unjudged"},"rows":[{"origin":"signal","id":"cmuxiucks11vjad0777gjfvwi","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"","relatedId":"","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/cli-help","severity":null,"label":"CLI help","detail":null,"valueNum":null,"valueText":"present","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiubn511orad071prfc2k9","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"","relatedId":"","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-environment-assumptions","severity":null,"label":"Declared environment assumptions","detail":null,"valueNum":null,"valueText":"Bundled scripts require Python 3.10+ and ete4 4.4.0 (upstream metadata requires Python >=3.7). Public taxonomy acquisition needs internet access. SmartView uses a local browser/server; static PNG rendering needs ete4[render-sm] and Chrome/Chromium, and Qt PDF/SVG rendering needs ete4[treeview].","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiuc7711t7ad07r3akwpg5","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"","relatedId":"","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-name","severity":null,"label":"Declared skill name","detail":null,"valueNum":null,"valueText":"etetoolkit","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiubtc11qhad07xphgse77","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"declared_tool","relatedId":"Bash","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Bash","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiubvv11r2ad07graz55d7","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"declared_tool","relatedId":"Edit","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Edit","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiubyh11rkad07y86w5107","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"declared_tool","relatedId":"Python","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Python","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiuc1211s1ad073yqvvu1e","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"declared_tool","relatedId":"Read","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Read","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiuc1e11s9ad07qxb7ua5e","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"declared_tool","relatedId":"Write","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Write","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiucn711vuad0736peveoq","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"","relatedId":"","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/interactive-prompts","severity":"high","label":"Interactive prompts detected","detail":"Agents run in non-interactive shells — replace prompts with CLI flags or stdin","valueNum":null,"valueText":null,"unit":null,"method":null,"derivation":null,"confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null},{"origin":"signal","id":"cmuxiucl111voad079vvku7zv","subjectType":"skill_audit","subjectId":"cmuxiub9y11lyad074e2mw4a7","relatedType":"","relatedId":"","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/structured-output","severity":null,"label":"Structured output","detail":null,"valueNum":null,"valueText":"present","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T03:01:47.000Z","payload":null}]},{"category":"sentiment","label":"Popularity","form":"unjudged","verdict":null,"rows":[]},{"category":"characteristics","label":"Characteristics","form":"unjudged","verdict":null,"rows":[]}],"signalCount":32,"publisherSupplied":["name","description","author","version","license"]}