phylogenetics
Pass
Audited by Gen Agent Trust Hub on Oct 24, 2026
Risk Level: SAFECOMMAND_EXECUTIONINDIRECT_PROMPT_INJECTION
Full Analysis
- [COMMAND_EXECUTION]: The script
scripts/phylogenetic_analysis.pyexecutes external bioinformatics binaries (mafft,iqtree3,FastTree) using thesubprocessmodule.\n - The commands are called using lists of arguments, which correctly avoids shell injection risks.\n
- Input FASTA files are validated for structural integrity before being passed to these external tools.\n- [INDIRECT_PROMPT_INJECTION]: The skill processes user-provided FASTA files, which introduces an attack surface for indirect prompt injection.\n
- Ingestion points: Sequences and identifiers are read from FASTA files in
scripts/phylogenetic_analysis.py.\n - Boundary markers (absent): The script enforces strict formatting but does not utilize explicit delimiters or "ignore embedded instructions" warnings for the data context.\n
- Capability inventory: The script performs local file writes and executes bioinformatics software via subprocesses.\n
- Sanitization (present): The
validate_fastafunction implements strict checks, rejecting whitespace and Newick-specific characters in identifiers and enforcing standard nucleotide/amino acid alphabets.
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