phylogenetics
Pass
Audited by Gen Agent Trust Hub on Sep 15, 2026
Risk Level: SAFECOMMAND_EXECUTIONEXTERNAL_DOWNLOADS
Full Analysis
- [COMMAND_EXECUTION]: The skill executes external bioinformatics binaries (MAFFT, IQ-TREE 2, FastTree, TrimAl) using the Python
subprocess.runmodule. The implementation correctly passes commands as lists rather than strings, which is a secure practice that prevents shell injection vulnerabilities. User-provided input such as file paths and sequence types are handled within these lists, significantly reducing the risk of command manipulation. - [EXTERNAL_DOWNLOADS]: The skill provides instructions for installing necessary software via standard package managers (Conda, Pip) and the reputable Bioconda channel. All referenced URLs in the documentation point to official software websites and well-known bioinformatics academic sites, which are trusted sources for these tools.
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