The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill facilitates the download of the NCBI taxonomy database (~~300MB) from official NCBI servers to a local cache (~~/.etetoolkit/taxa.sqlite) when the NCBITaxa class is instantiated for the first time. This is a standard and documented feature of the ETE toolkit used to retrieve taxonomic lineages and scientific names.
[COMMAND_EXECUTION]: The skill provides Python scripts (scripts/tree_operations.py and scripts/quick_visualize.py) that serve as command-line wrappers for tree manipulation and visualization. It also includes documentation for installing necessary system-level rendering dependencies (such as PyQt5 and SVG support) using standard package managers like apt-get and brew.
[INDIRECT_PROMPT_INJECTION]: The skill processes external biological data files, creating a surface for potential indirect prompt injection if those files contain malicious instructions.
Ingestion points: Data enters the agent's context through file parsing methods in ete3.Tree, ete3.PhyloTree, and ete3.ClusterTree (e.g., in SKILL.md and scripts/tree_operations.py).
Boundary markers: Absent; the toolkit parses standard formats (Newick, NHX, FASTA) where node names or features are treated as data for analysis and visualization.
Capability inventory: The skill has the capability to write files to the local system (tree.write, tree.render) and perform network updates for the taxonomy database.
Sanitization: Absent; the skill relies on the standard ete3 library parsers for format validation, but does not implement additional filtering for natural language instructions that might be embedded in node metadata.

etetoolkit