The Agent Skills Directory

[COMMAND_EXECUTION]: The skill implements wrappers for MAFFT, IQ-TREE, and FastTree using the Python subprocess.run function. The implementation correctly passes arguments as lists rather than raw strings, which prevents shell injection vulnerabilities by ensuring arguments are not interpreted by a shell environment.
[EXTERNAL_DOWNLOADS]: The skill documentation and scripts reference software installation via bioconda and PyPI. These are established and trusted repositories for scientific and Python software. The use of uv and conda for dependency management aligns with standard scientific computing practices.
[SAFE]: The skill does not exhibit patterns of data exfiltration, hardcoded credentials, or persistence mechanisms. The code is transparent and aligned with its described scientific purpose.
[INDIRECT_PROMPT_INJECTION]: The skill includes functionality to process FASTA files containing biological sequences. 1. Ingestion points: The input_fasta parameter in SKILL.md and script arguments. 2. Boundary markers: Not present. 3. Capability inventory: The skill can execute local binaries via subprocess.run. 4. Sanitization: None; it relies on the bioinformatic tools to validate sequence data formats.

phylogenetics