phylogenetics
https://raw.githubusercontent.com/k-dense-ai/scientific-agent-skills/main/skills/phylogenetics/SKILL.md
github.com/k-dense-ai/scientific-agent-skills
Scanned Thu, 28 May 2026 17:47:14 GMT
Scan ID crawl-l8jj79hqsbkuvigkmpv8wtlt · 3ms
B
SCORE 75 / 100
Verdict: Safe to install

5 medium findings.

This skill spawns subprocesses outside its declared capabilities plus 4 other issues listed below.

0 critical0 high5 medium7 rules passed

Why grade B?

score · 75 / 100

The current grade reflects 5 medium findings (3+ MEDs → B).

0 CRIT0 HIGH5 MED0 LOW
To reach a higher grade
  • A
    Reach Atarget score 95

    Resolve 3 of 5 MED (cap is 2).

Thresholds are documented at /docs/grading. Source-of-truth is the grade() function in @skillox/scanner.

Findings · ordered by severity

med
Arbitrary subprocess execution detected
The skill spawns subprocesses. Without a capability manifest declaring this, the skill could execute arbitrary commands.
rule: subprocess-executionline: 77CWE-78
▾
75
76 with open(output_fasta, 'w') as out:
77 result = subprocess.run(cmd, stdout=out, stderr=subprocess.PIPE, text=True)← spawns a subprocess outside declared capabilities
78
79 if result.returncode != 0:
med
Arbitrary subprocess execution detected
The skill spawns subprocesses. Without a capability manifest declaring this, the skill could execute arbitrary commands.
rule: subprocess-executionline: 110CWE-78
▾
108 """
109 cmd = ["trimal", f"-{method}", "-in", aligned_fasta, "-out", output_fasta, "-fasta"]
110 result = subprocess.run(cmd, capture_output=True, text=True)← spawns a subprocess outside declared capabilities
111 if result.returncode != 0:
112 print(f"TrimAl warning: {result.stderr}")
med
Arbitrary subprocess execution detected
The skill spawns subprocesses. Without a capability manifest declaring this, the skill could execute arbitrary commands.
rule: subprocess-executionline: 153CWE-78
▾
151 cmd.extend(extra_args)
152
153 result = subprocess.run(cmd, capture_output=True, text=True)← spawns a subprocess outside declared capabilities
154
155 if result.returncode != 0:
med
Arbitrary subprocess execution detected
The skill spawns subprocesses. Without a capability manifest declaring this, the skill could execute arbitrary commands.
rule: subprocess-executionline: 208CWE-78
▾
206
207 with open(output_tree, 'w') as out:
208 result = subprocess.run(cmd, stdout=out, stderr=subprocess.PIPE, text=True)← spawns a subprocess outside declared capabilities
209
210 if result.returncode != 0:
med
No capability manifest declared
The skill ships without a `manifest.yaml` or `capabilities` block in its frontmatter. Without a manifest, the runtime cannot enforce what this skill is permitted to do.
rule: no-manifest
▾
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