Data Analysis

biopython-phylo

86100Total Score

Core Capability

84 / 100

Functional Suitability

11 / 12

Reliability

9 / 12

Performance & Context

7 / 8

Agent Usability

14 / 16

Human Usability

8 / 8

Security

10 / 12

Maintainability

9 / 12

Agent-Specific

16 / 20

Medical Task

20 / 20 Passed

91Converting phylogenetic tree files between Newick, NEXUS, and phyloXML formats

4/4

87Traversing a tree to locate clades, prune taxa, or reroot at a specific node/outgroup

4/4

85Read and write phylogenetic trees via Bio.Phylo with support for common formats (Newick/NEXUS/phyloXML)

4/4

85Tree manipulation utilities: traversal, clade selection, pruning, and rerooting

4/4

85End-to-end case for Read and write phylogenetic trees via Bio.Phylo with support for common formats (Newick/NEXUS/phyloXML)

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	Scientific integrity held because extraction and analysis outputs stayed tied to provided text, metadata, or runtime evidence rather than invented study findings.
Practice Boundaries	PASS	The archived review kept this package within Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics, not freeform inference detached from source data.
Methodological Ground	PASS	The legacy review kept the package aligned with its named analysis library, data structure, or processing workflow.
Code Usability	PASS	The legacy audit did not record a code-usability failure in the packaged analysis path.

Core Capability84 / 100 — 8 Categories

Functional Suitability

Related legacy finding for biopython-phylo: 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

9 / 12

75%

Performance & Context

The archived review left minor headroom in how this analysis workflow scales across heavier contexts.

7 / 8

88%

Agent Usability

Agent usability was strong, but the workflow could surface its entry conditions a little more directly.

14 / 16

88%

Human Usability

Human usability reached full score in the archived evaluation.

8 / 8

100%

Security

A modest security gap remained in the archived evaluation despite otherwise controlled workflow behavior.

10 / 12

83%

Maintainability

The analysis package is maintainable overall, though the archived score suggests modest cleanup headroom.

9 / 12

75%

Agent-Specific

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

16 / 20

80%

Core Capability Total84 / 100

Medical TaskExecution Average: 86.6 / 100 — Assertions: 20/20 Passed

Canonical

Converting phylogenetic tree files between Newick, NEXUS, and phyloXML formats

4/4 ✓

Variant A

Traversing a tree to locate clades, prune taxa, or reroot at a specific node/outgroup

4/4 ✓

Edge

Read and write phylogenetic trees via Bio.Phylo with support for common formats (Newick/NEXUS/phyloXML)

4/4 ✓

Variant B

Tree manipulation utilities: traversal, clade selection, pruning, and rerooting

4/4 ✓

Stress

End-to-end case for Read and write phylogenetic trees via Bio.Phylo with support for common formats (Newick/NEXUS/phyloXML)

4/4 ✓

Canonical✅ Pass

Converting phylogenetic tree files between Newick, NEXUS, and phyloXML formats

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

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

✅A1The biopython-phylo 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

Traversing a tree to locate clades, prune taxa, or reroot at a specific node/outgroup

Traversing a tree to locate clades, prune taxa, or reroot at a... remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.

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

✅A1The biopython-phylo 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

Read and write phylogenetic trees via Bio.Phylo with support for common formats (Newick/NEXUS/phyloXML)

Read and write phylogenetic trees via Bio.Phylo with support for... remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.

Basic 33/40|Specialized 52/60|Total 85/100

✅A1The biopython-phylo 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

Tree manipulation utilities: traversal, clade selection, pruning, and rerooting

Tree manipulation utilities: traversal, clade selection, pruning,... remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.

Basic 32/40|Specialized 53/60|Total 85/100

✅A1The biopython-phylo 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 Read and write phylogenetic trees via Bio.Phylo with support for common formats (Newick/NEXUS/phyloXML)

The archived run treated End-to-end case for Read and write phylogenetic trees via Bio.Phylo... as a bounded analysis workflow rather than a purely narrative instruction path.

Basic 29/40|Specialized 56/60|Total 85/100

✅A1The biopython-phylo 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 Total86.6 / 100

Key Strengths

Primary routing is Data Analysis with execution mode A
Static quality score is 84/100 and dynamic average is 78.6/100
Assertions and command execution outcomes are recorded per input for human review
Execution verification summary: No script verification was applicable