Data Analysis

etetoolkit

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.

87100Total Score

Core Capability

87 / 100

Functional Suitability

11 / 12

Reliability

10 / 12

Performance & Context

8 / 8

Agent Usability

14 / 16

Human Usability

8 / 8

Security

9 / 12

Maintainability

10 / 12

Agent-Specific

17 / 20

Medical Task

20 / 20 Passed

91Preprocess phylogenetic trees: convert formats (Newick/NHX/PhyloXML), reroot (midpoint/outgroup), prune taxa, and resolve polytomies before downstream analyses

4/4

87Detect evolutionary events in gene trees: infer duplication vs. speciation events and derive ortholog/paralog relationships for phylogenomics

4/4

86Tree I/O and manipulation

4/4

86Read/write: Newick, NHX, PhyloXML, NeXML

4/4

86End-to-end case for Tree I/O and manipulation

4/4

Veto GatesRequired pass for any deployment consideration

Skill Veto✓ All 4 gates passed

✓

Operational Stability

System remains stable across varied inputs and edge cases

PASS

✓

Structural Consistency

Output structure conforms to expected skill contract format

PASS

✓

Result Determinism

Equivalent inputs produce semantically equivalent outputs

PASS

✓

System Security

No prompt injection, data leakage, or unsafe tool use detected

PASS

Research Veto✅ PASS — Applicable

Dimension	Result	Detail
Scientific Integrity	PASS	The archived review kept this workflow anchored to supplied data fields and observable execution behavior, not fabricated results.
Practice Boundaries	PASS	The evaluated outputs stayed inside the ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree... and did not drift into unsupported interpretation beyond the available inputs.
Methodological Ground	PASS	Methodological grounding was preserved through the documented inputs, transformations, and expected artifacts.
Code Usability	PASS	The archived review preserved a usable code path with named scripts, expected inputs, and a recognizable output contract.

Core Capability87 / 100 — 8 Categories

Functional Suitability

Related legacy finding for etetoolkit: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency

11 / 12

92%

Reliability

The archived deduction in reliability traces back to: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency

10 / 12

83%

Performance & Context

Performance context reached full score in the archived evaluation.

8 / 8

100%

Agent Usability

The packaged analysis path is understandable, though the archived score suggests slightly clearer routing would help.

14 / 16

88%

Human Usability

The legacy audit gave full marks to human usability for this package.

8 / 8

100%

Security

The packaged workflow stayed safe overall, with only a small remaining deduction around boundary signaling.

9 / 12

75%

Maintainability

Maintainability stayed solid, with only limited room to simplify scripts, dependencies, or packaging structure.

10 / 12

83%

Agent-Specific

Agent specific was softened by the legacy issue 'Improve stress-case output rigor'. Stress and boundary scenarios show weaker consistency

17 / 20

85%

Core Capability Total87 / 100

Medical TaskExecution Average: 87.2 / 100 — Assertions: 20/20 Passed

Canonical

Preprocess phylogenetic trees: convert formats (Newick/NHX/PhyloXML), reroot (midpoint/outgroup), prune taxa, and resolve polytomies before downstream analyses

4/4 ✓

Variant A

Detect evolutionary events in gene trees: infer duplication vs. speciation events and derive ortholog/paralog relationships for phylogenomics

4/4 ✓

Edge

Tree I/O and manipulation

4/4 ✓

Variant B

Read/write: Newick, NHX, PhyloXML, NeXML

4/4 ✓

Stress

End-to-end case for Tree I/O and manipulation

4/4 ✓

Canonical✅ Pass

Preprocess phylogenetic trees: convert formats (Newick/NHX/PhyloXML), reroot (midpoint/outgroup), prune taxa, and resolve polytomies before downstream analyses

The archived run treated Preprocess phylogenetic trees: convert formats... as a bounded analysis workflow rather than a purely narrative instruction path.

Basic 36/40|Specialized 55/60|Total 91/100

✅A1The etetoolkit output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Variant A✅ Pass

Detect evolutionary events in gene trees: infer duplication vs. speciation events and derive ortholog/paralog relationships for phylogenomics

The archived run treated Detect evolutionary events in gene trees: infer duplication vs.... as a bounded analysis workflow rather than a purely narrative instruction path.

Basic 34/40|Specialized 53/60|Total 87/100

✅A1The etetoolkit output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Edge✅ Pass

Tree I/O and manipulation

Tree I/O and manipulation remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.

Basic 33/40|Specialized 53/60|Total 86/100

✅A1The etetoolkit output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Variant B✅ Pass

Read/write: Newick, NHX, PhyloXML, NeXML

The archived run treated Read/write: Newick, NHX, PhyloXML, NeXML as a bounded analysis workflow rather than a purely narrative instruction path.

Basic 32/40|Specialized 54/60|Total 86/100

✅A1The etetoolkit output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Stress✅ Pass

End-to-end case for Tree I/O and manipulation

This stress case stayed within the packaged analysis boundary and kept a reviewable task contract.

Basic 29/40|Specialized 57/60|Total 86/100

✅A1The etetoolkit output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Medical Task Total87.2 / 100

Key Strengths

Primary routing is Data Analysis with execution mode B
Static quality score is 87/100 and dynamic average is 78.6/100
Assertions and command execution outcomes are recorded per input for human review
Execution verification summary: Script verification 0/2; adjustment=0. quick_visualize.py: rc=1; tree_operations.py: rc=1