The Agent Skills Directory

[COMMAND_EXECUTION]: The skill employs a local Python helper script (scripts/run_phylogenomics.py) to manage a pipeline of bioinformatics tools, including MAFFT, trimAl, IQ-TREE 3, and VeryFastTree. The script constructs and runs shell commands using subprocess.run based on input manifests.
[INDIRECT_PROMPT_INJECTION]: The skill ingests untrusted genomic sequence data and phylogenetic tree files that could contain adversarial content designed to influence the agent's behavior.
Ingestion points: The agent reads markers.tsv, FASTA sequences, and Newick-formatted tree files (.nwk, .treefile) during analysis and post-processing.
Boundary markers: The skill does not explicitly define or use delimiters (like XML tags or markdown blocks) to isolate sequence data or tree labels from the rest of the agent's instructions.
Capability inventory: The skill can execute specific command-line tools and write various TSV, JSON, and report files to the filesystem.
Sanitization: The script implements checksum validation for reference sequences to ensure data integrity before processing.
[EXTERNAL_DOWNLOADS]: The skill instructions involve fetching genome and proteome sequences from external biological databases (e.g., NCBI) to support comparative analysis.

bio-phylogenomics