The Agent Skills Directory

[COMMAND_EXECUTION]: Several scripts, including phykit_batch.py, scogs_paired_compare.py, and scogs_phykit_pipeline.py, use the subprocess.run function to execute the phykit command-line utility. These calls are implemented using argument lists and do not invoke a shell environment (no shell=True), which mitigates command injection risks. The functions executed via phykit are limited to a predefined set of bioinformatics subcommands.
[INDIRECT_PROMPT_INJECTION]: The skill processes biological data files such as FASTA, Newick, and ZIP archives. These represent ingestion points for external data. However, the skill utilizes standard, well-maintained libraries like Biopython and DendroPy for parsing, and the extraction logic in busco_target_orthologs.py explicitly filters for specific directory structures and file extensions (.faa) within the archives.
[SAFE]: The skill's behavior is consistent with its stated purpose of phylogenetic analysis and comparative genomics. The scripts facilitate local processing of scientific data without hardcoded credentials, persistence mechanisms, or unauthorized network operations. The code is authored by a recognized academic entity (MIMS Harvard).

tooluniverse-phylogenetics