Skills biopython Audit History
📦

Audit History

biopython - 7 audits

Version comparison

Capability and finding changes across audited versions, newest first.

VersionDateResultReview itemsChange vs previous
v7 LatestJul 5, 2026, 06:16 PM No confirmed findings0No capability change
v6 Jul 5, 2026, 06:16 PM No confirmed findings0No capability change
v5 Jun 30, 2026, 05:56 AM 3 confirmed1No capability change
v4 Jan 17, 2026, 05:49 AM No confirmed findings0No capability change
v3 Jan 17, 2026, 05:49 AM No confirmed findings0Env variables
v2 Jan 12, 2026, 04:20 PM No confirmed findings0External commandsFilesystem accessNetwork access
v1 Jan 5, 2026, 04:01 PM No confirmed findings0Baseline

Jul 5, 2026, 06:16 PM

All static findings were adjudicated as false positives after reviewing the referenced documentation context. The skill is a Markdown guidance package for Biopython workflows, and I found no prompt injection, credential exfiltration, hidden execution, or malicious network intent.

9
Files scanned
3,935
Lines analyzed
4
Review items
0
False positives ignored
Audited by: codex

Jul 5, 2026, 06:16 PM

All static findings were adjudicated as false positives after reviewing the referenced documentation context. The skill is a Markdown guidance package for Biopython workflows, and I found no prompt injection, credential exfiltration, hidden execution, or malicious network intent.

9
Files scanned
3,935
Lines analyzed
4
Review items
0
False positives ignored
Audited by: codex

Jun 30, 2026, 05:56 AM

Static analysis produced a risk score of 100 because it treated markdown code fences, Biopython examples, placeholders, and scientific terms as dangerous code. Human review found no malicious intent or prompt injection, but the skill legitimately documents network calls, file I/O, API key configuration, and local BLAST command wrappers, so publication should carry a medium-risk warning.

9
Files scanned
3,935
Lines analyzed
8
Review items
3
False positives ignored

Confirmed security concerns (3)

Medium
Legitimate External Network Access Examples
The skill documents Bio.Entrez and NCBIWWW.qblast calls that contact NCBI web services. This is expected for bioinformatics workflows, but generated code may send sequence queries or identifiers to external services.
The cited examples directly call NCBI web APIs. The purpose is legitimate and documented, with no evidence of hidden endpoints or exfiltration.
Medium
Local BLAST Command Wrapper Examples
The BLAST reference demonstrates Biopython command-line wrappers that invoke installed BLAST+ binaries. This is a real external command capability when users run generated code, but the arguments are normal bioinformatics parameters rather than obfuscated commands.
The documentation explicitly constructs command-line wrapper objects and executes them. The examples are transparent and aligned with local BLAST use.
Low
File Read and Write Examples
The references show normal parsing and output patterns for FASTA, BLAST XML, JASPAR, and related scientific files. These examples can write local files when users run generated code, so users should choose paths deliberately.
The locations are conventional file I/O examples. They are not malicious, but they are real operations if copied into executable code.
Capability review items (1)

These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.

Low
Placeholder API Key Guidance
Static analysis flagged API key text, but the cited content uses placeholders for NCBI Entrez configuration. No real secret was found, and there is no code that collects or transmits arbitrary credentials.
The evidence contains placeholder strings such as an example email and API key. No actual credential material or exfiltration flow was identified.
Static false positives ignored (3)

These static matches were dismissed by semantic review or matched schema-only tokens, so they are shown for transparency but do not drive the quality score.

Low
Markdown Backticks Misclassified as Shell Execution
Most external-command alerts appear to come from markdown code fence delimiters and command examples in documentation. The skill files are references, not scripts that execute backtick substitutions automatically.
The cited lines are documentation fences or a prior static-evaluation explanation. They do not create an execution path by themselves.
Low
Weak Cryptography Alerts Are Domain False Positives
The weak-cryptography alerts align with scientific documentation terms and markdown references, not password hashing or encryption logic. No evidence found of MD5, SHA-1, DES, or similar cryptography used for security decisions.
The alerts occur inside bioinformatics documentation rather than authentication or cryptographic code. I did not find security-sensitive crypto usage.
Low
System Reconnaissance Alerts Are Documentation Context
System reconnaissance alerts correspond to scientific file parsing, database statistics, or structure inspection examples. No evidence found of host enumeration, privilege discovery, or environment harvesting.
The static labels are weak signals in documentation examples. I found no semantic evidence of host reconnaissance intent.

Detected Patterns

Legitimate External Network Access ExamplesLocal BLAST Command Wrapper ExamplesFile Read and Write Examples
Audited by: codex

Jan 17, 2026, 05:49 AM

All 546 static findings are FALSE POSITIVES. This skill contains only markdown documentation files with Python code examples for Biopython. The scanner misidentified markdown code block delimiters as shell commands, Biopython module names (Bio.Align, Bio.Phylo) as cryptographic algorithms, and documentation placeholders as real secrets. No executable code exists. This is a legitimate scientific documentation skill.

8
Files scanned
3,743
Lines analyzed
4
Review items
0
False positives ignored

Risk Factors

🔑 Env variables (6)
⚙️ External commands (415)
references/advanced.md:7-23 references/advanced.md:23-27 references/advanced.md:27-36 references/advanced.md:36-40 references/advanced.md:40-48 references/advanced.md:48-52 references/advanced.md:52-64 references/advanced.md:64-68 references/advanced.md:68-79 references/advanced.md:79-83 references/advanced.md:83-87 references/advanced.md:87-93 references/advanced.md:93-109 references/advanced.md:109-113 references/advanced.md:113-128 references/advanced.md:128-134 references/advanced.md:134-141 references/advanced.md:141-145 references/advanced.md:145-157 references/advanced.md:157-161 references/advanced.md:161-174 references/advanced.md:174-178 references/advanced.md:178-185 references/advanced.md:185-189 references/advanced.md:189-219 references/advanced.md:219-223 references/advanced.md:223-245 references/advanced.md:245-249 references/advanced.md:249-267 references/advanced.md:267-271 references/advanced.md:271-287 references/advanced.md:287-291 references/advanced.md:291-325 references/advanced.md:325-333 references/advanced.md:333-343 references/advanced.md:343-347 references/advanced.md:347-363 references/advanced.md:363-367 references/advanced.md:367-387 references/advanced.md:387-391 references/advanced.md:391-403 references/advanced.md:403-407 references/advanced.md:407-424 references/advanced.md:424-443 references/advanced.md:443-483 references/advanced.md:483-487 references/advanced.md:487-509 references/advanced.md:509-513 references/advanced.md:513-542 references/advanced.md:542-546 references/advanced.md:546-577 references/alignment.md:11 references/alignment.md:15-25 references/alignment.md:25-29 references/alignment.md:29-48 references/alignment.md:48-52 references/alignment.md:52-58 references/alignment.md:58-62 references/alignment.md:62-78 references/alignment.md:78-82 references/alignment.md:82-93 references/alignment.md:93-102 references/alignment.md:102-106 references/alignment.md:106-114 references/alignment.md:114-124 references/alignment.md:124-141 references/alignment.md:141-147 references/alignment.md:147-151 references/alignment.md:151-172 references/alignment.md:172-176 references/alignment.md:176-192 references/alignment.md:192-198 references/alignment.md:198-212 references/alignment.md:212-216 references/alignment.md:216-226 references/alignment.md:226-232 references/alignment.md:232-241 references/alignment.md:241-245 references/alignment.md:245-249 references/alignment.md:249-253 references/alignment.md:253-265 references/alignment.md:265-271 references/alignment.md:271-287 references/alignment.md:287-291 references/alignment.md:291-299 references/alignment.md:299-315 references/alignment.md:315-329 references/alignment.md:329-333 references/alignment.md:333-344 references/alignment.md:344-348 references/alignment.md:348-362 references/blast.md:11 references/blast.md:13-31 references/blast.md:31-44 references/blast.md:44-45 references/blast.md:45-48 references/blast.md:48-49 references/blast.md:49-50 references/blast.md:50-51 references/blast.md:51-55 references/blast.md:55-67 references/blast.md:67-71 references/blast.md:71-81 references/blast.md:81-89 references/blast.md:89-95 references/blast.md:95-99 references/blast.md:99-122 references/blast.md:122-126 references/blast.md:126-137 references/blast.md:137-143 references/blast.md:143-159 references/blast.md:159-171 references/blast.md:171-190 references/blast.md:190-194 references/blast.md:194-195 references/blast.md:195-196 references/blast.md:196-197 references/blast.md:197-198 references/blast.md:198-202 references/blast.md:202-212 references/blast.md:212-218 references/blast.md:218-240 references/blast.md:240-244 references/blast.md:244-255 references/blast.md:255-259 references/blast.md:259-284 references/blast.md:284-290 references/blast.md:290-311 references/blast.md:311-315 references/blast.md:315-323 references/blast.md:323-342 references/blast.md:342-363 references/blast.md:363-367 references/blast.md:367-391 references/blast.md:391-395 references/blast.md:395-415 references/blast.md:415-419 references/blast.md:419-439 references/blast.md:439-443 references/blast.md:443-455 references/databases.md:13-18 references/databases.md:18-24 references/databases.md:24-27 references/databases.md:27-43 references/databases.md:43-54 references/databases.md:54-60 references/databases.md:60-70 references/databases.md:70-74 references/databases.md:74-86 references/databases.md:86-92 references/databases.md:92-103 references/databases.md:103-109 references/databases.md:109-121 references/databases.md:121-128 references/databases.md:128-129 references/databases.md:129 references/databases.md:129-130 references/databases.md:130-133 references/databases.md:133-134 references/databases.md:134-137 references/databases.md:137-138 references/databases.md:138-144 references/databases.md:144-155 references/databases.md:155-161 references/databases.md:161-180 references/databases.md:180-186 references/databases.md:186-193 references/databases.md:193-199 references/databases.md:199-206 references/databases.md:206-212 references/databases.md:212-228 references/databases.md:228-232 references/databases.md:232-248 references/databases.md:248-252 references/databases.md:252-270 references/databases.md:270-274 references/databases.md:274-284 references/databases.md:284-288 references/databases.md:288-303 references/databases.md:303-309 references/databases.md:309-318 references/databases.md:318-322 references/databases.md:322-346 references/databases.md:346-352 references/databases.md:352-381 references/databases.md:381-385 references/databases.md:385-391 references/databases.md:391-408 references/databases.md:408-422 references/databases.md:422-428 references/databases.md:428-443 references/databases.md:443-447 references/databases.md:447-464 references/databases.md:464-468 references/databases.md:468-484 references/phylogenetics.md:19-28 references/phylogenetics.md:28-32 references/phylogenetics.md:32-38 references/phylogenetics.md:38-42 references/phylogenetics.md:42-46 references/phylogenetics.md:46-60 references/phylogenetics.md:60-75 references/phylogenetics.md:75-79 references/phylogenetics.md:79-96 references/phylogenetics.md:96-100 references/phylogenetics.md:100-109 references/phylogenetics.md:109-115 references/phylogenetics.md:115-128 references/phylogenetics.md:128-132 references/phylogenetics.md:132-153 references/phylogenetics.md:153-157 references/phylogenetics.md:157-167 references/phylogenetics.md:167-171 references/phylogenetics.md:171-194 references/phylogenetics.md:194-200 references/phylogenetics.md:200-211 references/phylogenetics.md:211-215 references/phylogenetics.md:215-223 references/phylogenetics.md:223-227 references/phylogenetics.md:227-231 references/phylogenetics.md:231-235 references/phylogenetics.md:235-246 references/phylogenetics.md:246-252 references/phylogenetics.md:252-258 references/phylogenetics.md:258-262 references/phylogenetics.md:262-279 references/phylogenetics.md:279-283 references/phylogenetics.md:283-300 references/phylogenetics.md:300-306 references/phylogenetics.md:306-327 references/phylogenetics.md:327-331 references/phylogenetics.md:331-348 references/phylogenetics.md:348-359 references/phylogenetics.md:359-363 references/phylogenetics.md:363-367 references/phylogenetics.md:367-381 references/phylogenetics.md:381-387 references/phylogenetics.md:387-405 references/phylogenetics.md:405-409 references/phylogenetics.md:409-421 references/phylogenetics.md:421-430 references/phylogenetics.md:430-440 references/phylogenetics.md:440-466 references/phylogenetics.md:466-470 references/phylogenetics.md:470-489 references/phylogenetics.md:489-493 references/phylogenetics.md:493-515 references/phylogenetics.md:515-519 references/phylogenetics.md:519-539 references/phylogenetics.md:539-543 references/phylogenetics.md:543-566 references/sequence_io.md:5 references/sequence_io.md:11-20 references/sequence_io.md:20-24 references/sequence_io.md:24-37 references/sequence_io.md:37-41 references/sequence_io.md:41-42 references/sequence_io.md:42-43 references/sequence_io.md:43-44 references/sequence_io.md:44-45 references/sequence_io.md:45-46 references/sequence_io.md:46-47 references/sequence_io.md:47-53 references/sequence_io.md:53-55 references/sequence_io.md:55-63 references/sequence_io.md:63-67 references/sequence_io.md:67-69 references/sequence_io.md:69-73 references/sequence_io.md:73-77 references/sequence_io.md:77-81 references/sequence_io.md:81-84 references/sequence_io.md:84-99 references/sequence_io.md:99-101 references/sequence_io.md:101-109 references/sequence_io.md:109-113 references/sequence_io.md:113-123 references/sequence_io.md:123-131 references/sequence_io.md:131-136 references/sequence_io.md:136-144 references/sequence_io.md:144-147 references/sequence_io.md:147-151 references/sequence_io.md:151-155 references/sequence_io.md:155-159 references/sequence_io.md:159-163 references/sequence_io.md:163-169 references/sequence_io.md:169-181 references/sequence_io.md:181-187 references/sequence_io.md:187-196 references/sequence_io.md:196-202 references/sequence_io.md:202-214 references/sequence_io.md:214-218 references/sequence_io.md:218-223 references/sequence_io.md:223-240 references/sequence_io.md:240-247 references/sequence_io.md:247-251 references/sequence_io.md:251-257 references/sequence_io.md:257-261 references/sequence_io.md:261-267 references/sequence_io.md:267-271 references/sequence_io.md:271-285 references/structure.md:11-17 references/structure.md:17-23 references/structure.md:23-35 references/structure.md:35-41 references/structure.md:41-49 references/structure.md:49-53 references/structure.md:53-67 references/structure.md:67-73 references/structure.md:73-80 references/structure.md:80-84 references/structure.md:84-91 references/structure.md:91-95 references/structure.md:95-103 references/structure.md:103-107 references/structure.md:107-115 references/structure.md:115-119 references/structure.md:119-132 references/structure.md:132-138 references/structure.md:138-151 references/structure.md:151-155 references/structure.md:155-164 references/structure.md:164-168 references/structure.md:168-178 references/structure.md:178-182 references/structure.md:182-193 references/structure.md:193-201 references/structure.md:201-220 references/structure.md:220-223 references/structure.md:223-224 references/structure.md:224-225 references/structure.md:225-226 references/structure.md:226-227 references/structure.md:227-228 references/structure.md:228-229 references/structure.md:229-230 references/structure.md:230-234 references/structure.md:234-239 references/structure.md:239-245 references/structure.md:245-264 references/structure.md:264-268 references/structure.md:268-286 references/structure.md:286-292 references/structure.md:292-309 references/structure.md:309-313 references/structure.md:313-330 references/structure.md:330-336 references/structure.md:336-356 references/structure.md:356-360 references/structure.md:360-376 references/structure.md:376-380 references/structure.md:380-408 references/structure.md:408-414 references/structure.md:414-420 references/structure.md:420-424 references/structure.md:424-430 references/structure.md:430-436 references/structure.md:436-447 references/structure.md:447-451 references/structure.md:451-470 references/structure.md:470-489 references/structure.md:489-509 references/structure.md:509-513 references/structure.md:513-539 references/structure.md:539-543 references/structure.md:543-564 SKILL.md:48-50 SKILL.md:50-54 SKILL.md:54-60 SKILL.md:60-68 SKILL.md:68-79 SKILL.md:79-88 SKILL.md:88-92 SKILL.md:92-102 SKILL.md:102-110 SKILL.md:110-114 SKILL.md:114-124 SKILL.md:124-133 SKILL.md:133-137 SKILL.md:137-147 SKILL.md:147-157 SKILL.md:157-161 SKILL.md:161-172 SKILL.md:172-183 SKILL.md:183-187 SKILL.md:187-198 SKILL.md:198-208 SKILL.md:208-212 SKILL.md:212-223 SKILL.md:223-230 SKILL.md:230-244 SKILL.md:244-253 SKILL.md:253-260 SKILL.md:260-263 SKILL.md:263-266 SKILL.md:266-268 SKILL.md:268-271 SKILL.md:271-273 SKILL.md:273-276 SKILL.md:276-279 SKILL.md:279-282 SKILL.md:282-285 SKILL.md:285-288 SKILL.md:288-293 SKILL.md:293-299 SKILL.md:299-311 SKILL.md:311-315 SKILL.md:315-328 SKILL.md:328-332 SKILL.md:332-351 SKILL.md:351-355 SKILL.md:355-372 SKILL.md:372-405 SKILL.md:405-419 SKILL.md:419-428 SKILL.md:428-435
📁 Filesystem access (6)
🌐 Network access (6)
Audited by: claude

Jan 17, 2026, 05:49 AM

All 546 static findings are FALSE POSITIVES. This skill contains only markdown documentation files with Python code examples for Biopython. The scanner misidentified markdown code block delimiters as shell commands, Biopython module names (Bio.Align, Bio.Phylo) as cryptographic algorithms, and documentation placeholders as real secrets. No executable code exists. This is a legitimate scientific documentation skill.

8
Files scanned
3,743
Lines analyzed
4
Review items
0
False positives ignored

Risk Factors

🔑 Env variables (6)
⚙️ External commands (415)
references/advanced.md:7-23 references/advanced.md:23-27 references/advanced.md:27-36 references/advanced.md:36-40 references/advanced.md:40-48 references/advanced.md:48-52 references/advanced.md:52-64 references/advanced.md:64-68 references/advanced.md:68-79 references/advanced.md:79-83 references/advanced.md:83-87 references/advanced.md:87-93 references/advanced.md:93-109 references/advanced.md:109-113 references/advanced.md:113-128 references/advanced.md:128-134 references/advanced.md:134-141 references/advanced.md:141-145 references/advanced.md:145-157 references/advanced.md:157-161 references/advanced.md:161-174 references/advanced.md:174-178 references/advanced.md:178-185 references/advanced.md:185-189 references/advanced.md:189-219 references/advanced.md:219-223 references/advanced.md:223-245 references/advanced.md:245-249 references/advanced.md:249-267 references/advanced.md:267-271 references/advanced.md:271-287 references/advanced.md:287-291 references/advanced.md:291-325 references/advanced.md:325-333 references/advanced.md:333-343 references/advanced.md:343-347 references/advanced.md:347-363 references/advanced.md:363-367 references/advanced.md:367-387 references/advanced.md:387-391 references/advanced.md:391-403 references/advanced.md:403-407 references/advanced.md:407-424 references/advanced.md:424-443 references/advanced.md:443-483 references/advanced.md:483-487 references/advanced.md:487-509 references/advanced.md:509-513 references/advanced.md:513-542 references/advanced.md:542-546 references/advanced.md:546-577 references/alignment.md:11 references/alignment.md:15-25 references/alignment.md:25-29 references/alignment.md:29-48 references/alignment.md:48-52 references/alignment.md:52-58 references/alignment.md:58-62 references/alignment.md:62-78 references/alignment.md:78-82 references/alignment.md:82-93 references/alignment.md:93-102 references/alignment.md:102-106 references/alignment.md:106-114 references/alignment.md:114-124 references/alignment.md:124-141 references/alignment.md:141-147 references/alignment.md:147-151 references/alignment.md:151-172 references/alignment.md:172-176 references/alignment.md:176-192 references/alignment.md:192-198 references/alignment.md:198-212 references/alignment.md:212-216 references/alignment.md:216-226 references/alignment.md:226-232 references/alignment.md:232-241 references/alignment.md:241-245 references/alignment.md:245-249 references/alignment.md:249-253 references/alignment.md:253-265 references/alignment.md:265-271 references/alignment.md:271-287 references/alignment.md:287-291 references/alignment.md:291-299 references/alignment.md:299-315 references/alignment.md:315-329 references/alignment.md:329-333 references/alignment.md:333-344 references/alignment.md:344-348 references/alignment.md:348-362 references/blast.md:11 references/blast.md:13-31 references/blast.md:31-44 references/blast.md:44-45 references/blast.md:45-48 references/blast.md:48-49 references/blast.md:49-50 references/blast.md:50-51 references/blast.md:51-55 references/blast.md:55-67 references/blast.md:67-71 references/blast.md:71-81 references/blast.md:81-89 references/blast.md:89-95 references/blast.md:95-99 references/blast.md:99-122 references/blast.md:122-126 references/blast.md:126-137 references/blast.md:137-143 references/blast.md:143-159 references/blast.md:159-171 references/blast.md:171-190 references/blast.md:190-194 references/blast.md:194-195 references/blast.md:195-196 references/blast.md:196-197 references/blast.md:197-198 references/blast.md:198-202 references/blast.md:202-212 references/blast.md:212-218 references/blast.md:218-240 references/blast.md:240-244 references/blast.md:244-255 references/blast.md:255-259 references/blast.md:259-284 references/blast.md:284-290 references/blast.md:290-311 references/blast.md:311-315 references/blast.md:315-323 references/blast.md:323-342 references/blast.md:342-363 references/blast.md:363-367 references/blast.md:367-391 references/blast.md:391-395 references/blast.md:395-415 references/blast.md:415-419 references/blast.md:419-439 references/blast.md:439-443 references/blast.md:443-455 references/databases.md:13-18 references/databases.md:18-24 references/databases.md:24-27 references/databases.md:27-43 references/databases.md:43-54 references/databases.md:54-60 references/databases.md:60-70 references/databases.md:70-74 references/databases.md:74-86 references/databases.md:86-92 references/databases.md:92-103 references/databases.md:103-109 references/databases.md:109-121 references/databases.md:121-128 references/databases.md:128-129 references/databases.md:129 references/databases.md:129-130 references/databases.md:130-133 references/databases.md:133-134 references/databases.md:134-137 references/databases.md:137-138 references/databases.md:138-144 references/databases.md:144-155 references/databases.md:155-161 references/databases.md:161-180 references/databases.md:180-186 references/databases.md:186-193 references/databases.md:193-199 references/databases.md:199-206 references/databases.md:206-212 references/databases.md:212-228 references/databases.md:228-232 references/databases.md:232-248 references/databases.md:248-252 references/databases.md:252-270 references/databases.md:270-274 references/databases.md:274-284 references/databases.md:284-288 references/databases.md:288-303 references/databases.md:303-309 references/databases.md:309-318 references/databases.md:318-322 references/databases.md:322-346 references/databases.md:346-352 references/databases.md:352-381 references/databases.md:381-385 references/databases.md:385-391 references/databases.md:391-408 references/databases.md:408-422 references/databases.md:422-428 references/databases.md:428-443 references/databases.md:443-447 references/databases.md:447-464 references/databases.md:464-468 references/databases.md:468-484 references/phylogenetics.md:19-28 references/phylogenetics.md:28-32 references/phylogenetics.md:32-38 references/phylogenetics.md:38-42 references/phylogenetics.md:42-46 references/phylogenetics.md:46-60 references/phylogenetics.md:60-75 references/phylogenetics.md:75-79 references/phylogenetics.md:79-96 references/phylogenetics.md:96-100 references/phylogenetics.md:100-109 references/phylogenetics.md:109-115 references/phylogenetics.md:115-128 references/phylogenetics.md:128-132 references/phylogenetics.md:132-153 references/phylogenetics.md:153-157 references/phylogenetics.md:157-167 references/phylogenetics.md:167-171 references/phylogenetics.md:171-194 references/phylogenetics.md:194-200 references/phylogenetics.md:200-211 references/phylogenetics.md:211-215 references/phylogenetics.md:215-223 references/phylogenetics.md:223-227 references/phylogenetics.md:227-231 references/phylogenetics.md:231-235 references/phylogenetics.md:235-246 references/phylogenetics.md:246-252 references/phylogenetics.md:252-258 references/phylogenetics.md:258-262 references/phylogenetics.md:262-279 references/phylogenetics.md:279-283 references/phylogenetics.md:283-300 references/phylogenetics.md:300-306 references/phylogenetics.md:306-327 references/phylogenetics.md:327-331 references/phylogenetics.md:331-348 references/phylogenetics.md:348-359 references/phylogenetics.md:359-363 references/phylogenetics.md:363-367 references/phylogenetics.md:367-381 references/phylogenetics.md:381-387 references/phylogenetics.md:387-405 references/phylogenetics.md:405-409 references/phylogenetics.md:409-421 references/phylogenetics.md:421-430 references/phylogenetics.md:430-440 references/phylogenetics.md:440-466 references/phylogenetics.md:466-470 references/phylogenetics.md:470-489 references/phylogenetics.md:489-493 references/phylogenetics.md:493-515 references/phylogenetics.md:515-519 references/phylogenetics.md:519-539 references/phylogenetics.md:539-543 references/phylogenetics.md:543-566 references/sequence_io.md:5 references/sequence_io.md:11-20 references/sequence_io.md:20-24 references/sequence_io.md:24-37 references/sequence_io.md:37-41 references/sequence_io.md:41-42 references/sequence_io.md:42-43 references/sequence_io.md:43-44 references/sequence_io.md:44-45 references/sequence_io.md:45-46 references/sequence_io.md:46-47 references/sequence_io.md:47-53 references/sequence_io.md:53-55 references/sequence_io.md:55-63 references/sequence_io.md:63-67 references/sequence_io.md:67-69 references/sequence_io.md:69-73 references/sequence_io.md:73-77 references/sequence_io.md:77-81 references/sequence_io.md:81-84 references/sequence_io.md:84-99 references/sequence_io.md:99-101 references/sequence_io.md:101-109 references/sequence_io.md:109-113 references/sequence_io.md:113-123 references/sequence_io.md:123-131 references/sequence_io.md:131-136 references/sequence_io.md:136-144 references/sequence_io.md:144-147 references/sequence_io.md:147-151 references/sequence_io.md:151-155 references/sequence_io.md:155-159 references/sequence_io.md:159-163 references/sequence_io.md:163-169 references/sequence_io.md:169-181 references/sequence_io.md:181-187 references/sequence_io.md:187-196 references/sequence_io.md:196-202 references/sequence_io.md:202-214 references/sequence_io.md:214-218 references/sequence_io.md:218-223 references/sequence_io.md:223-240 references/sequence_io.md:240-247 references/sequence_io.md:247-251 references/sequence_io.md:251-257 references/sequence_io.md:257-261 references/sequence_io.md:261-267 references/sequence_io.md:267-271 references/sequence_io.md:271-285 references/structure.md:11-17 references/structure.md:17-23 references/structure.md:23-35 references/structure.md:35-41 references/structure.md:41-49 references/structure.md:49-53 references/structure.md:53-67 references/structure.md:67-73 references/structure.md:73-80 references/structure.md:80-84 references/structure.md:84-91 references/structure.md:91-95 references/structure.md:95-103 references/structure.md:103-107 references/structure.md:107-115 references/structure.md:115-119 references/structure.md:119-132 references/structure.md:132-138 references/structure.md:138-151 references/structure.md:151-155 references/structure.md:155-164 references/structure.md:164-168 references/structure.md:168-178 references/structure.md:178-182 references/structure.md:182-193 references/structure.md:193-201 references/structure.md:201-220 references/structure.md:220-223 references/structure.md:223-224 references/structure.md:224-225 references/structure.md:225-226 references/structure.md:226-227 references/structure.md:227-228 references/structure.md:228-229 references/structure.md:229-230 references/structure.md:230-234 references/structure.md:234-239 references/structure.md:239-245 references/structure.md:245-264 references/structure.md:264-268 references/structure.md:268-286 references/structure.md:286-292 references/structure.md:292-309 references/structure.md:309-313 references/structure.md:313-330 references/structure.md:330-336 references/structure.md:336-356 references/structure.md:356-360 references/structure.md:360-376 references/structure.md:376-380 references/structure.md:380-408 references/structure.md:408-414 references/structure.md:414-420 references/structure.md:420-424 references/structure.md:424-430 references/structure.md:430-436 references/structure.md:436-447 references/structure.md:447-451 references/structure.md:451-470 references/structure.md:470-489 references/structure.md:489-509 references/structure.md:509-513 references/structure.md:513-539 references/structure.md:539-543 references/structure.md:543-564 SKILL.md:48-50 SKILL.md:50-54 SKILL.md:54-60 SKILL.md:60-68 SKILL.md:68-79 SKILL.md:79-88 SKILL.md:88-92 SKILL.md:92-102 SKILL.md:102-110 SKILL.md:110-114 SKILL.md:114-124 SKILL.md:124-133 SKILL.md:133-137 SKILL.md:137-147 SKILL.md:147-157 SKILL.md:157-161 SKILL.md:161-172 SKILL.md:172-183 SKILL.md:183-187 SKILL.md:187-198 SKILL.md:198-208 SKILL.md:208-212 SKILL.md:212-223 SKILL.md:223-230 SKILL.md:230-244 SKILL.md:244-253 SKILL.md:253-260 SKILL.md:260-263 SKILL.md:263-266 SKILL.md:266-268 SKILL.md:268-271 SKILL.md:271-273 SKILL.md:273-276 SKILL.md:276-279 SKILL.md:279-282 SKILL.md:282-285 SKILL.md:285-288 SKILL.md:288-293 SKILL.md:293-299 SKILL.md:299-311 SKILL.md:311-315 SKILL.md:315-328 SKILL.md:328-332 SKILL.md:332-351 SKILL.md:351-355 SKILL.md:355-372 SKILL.md:372-405 SKILL.md:405-419 SKILL.md:419-428 SKILL.md:428-435
📁 Filesystem access (6)
🌐 Network access (6)
Audited by: claude

Jan 12, 2026, 04:20 PM

All 525 static findings are FALSE POSITIVES. This is a documentation skill containing markdown files with Biopython code examples. The static analyzer flagged shell commands, file I/O, and network access patterns in documentation examples, but these represent legitimate bioinformatics operations in markdown files, not executable malicious code. No actual security risks present.

8
Files scanned
3,743
Lines analyzed
3
Review items
0
False positives ignored
Audited by: claude

Jan 5, 2026, 04:01 PM

This is a documentation-only skill that provides comprehensive information about Biopython, a legitimate bioinformatics Python library. The skill contains no executable code, network calls, file operations, or security-sensitive capabilities. It consists entirely of educational content and code examples for bioinformatics analysis.

11
Files scanned
4,050
Lines analyzed
0
Review items
0
False positives ignored
No confirmed security findings were recorded for this completed audit.
Audited by: claude