The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill facilitates the download of a large taxonomy database (~300MB) from the National Center for Biotechnology Information (NCBI) via the ete3.NCBITaxa class. This is a standard procedure for local taxonomy lookup and utilizes a well-known scientific service domain.
[COMMAND_EXECUTION]: The skill includes Python scripts (scripts/tree_operations.py and scripts/quick_visualize.py) intended for command-line use. These scripts allow the agent to execute complex tree manipulation and rendering tasks using provided file paths and parameters.
[INDIRECT_PROMPT_INJECTION]: The skill is designed to ingest and parse external data files in Newick and NHX formats, creating an indirect prompt injection surface.
Ingestion points: External files are loaded into the agent's context through the Tree and PhyloTree constructors in the provided scripts and documentation examples.
Boundary markers: The skill does not provide explicit delimiters or instructions to the agent to ignore potentially malicious content embedded within the scientific metadata of the tree files.
Capability inventory: The skill has capabilities for file system writes (tree.write, tree.render) and shell execution via provided utility scripts.
Sanitization: The skill relies on standard Newick parsing logic and does not implement additional validation or filtering of string content within the trees before it is processed by the agent.

alterlab-etetoolkit