The Agent Skills Directory

[COMMAND_EXECUTION]: The skill executes external bioinformatics command-line tools including MAFFT, IQ-TREE 2, and FastTree using the subprocess module.
Evidence: Functions in scripts/phylogenetic_analysis.py and SKILL.md (e.g., run_mafft, run_iqtree) use subprocess.run with list-based arguments.
This implementation is safe as it avoids the use of shell=True, effectively preventing command injection vulnerabilities from untrusted file names or parameters.
[EXTERNAL_DOWNLOADS]: The skill references the installation of scientific software from well-known community repositories.
Evidence: Installation instructions point to bioconda for mafft, iqtree, and fasttree, and to the Python Package Index (PyPI) for ete3 and PyQt5.
These are trusted sources within the biological research community.
[INDIRECT_PROMPT_INJECTION]: The skill defines a workflow that ingests biological sequence data from external FASTA files.
Evidence: The script reads FASTA files to count sequences and passes file paths to analysis tools.
The attack surface is minimal as the ingestion logic only counts lines starting with standard FASTA headers (>) and does not process the content as instructions.

phylogenetics