The Agent Skills Directory

[COMMAND_EXECUTION]: The documentation includes installation steps requiring sudo to install system packages (python3-pyqt5) necessary for graphical tree rendering.
[EXTERNAL_DOWNLOADS]: The skill uses the NCBITaxa module, which automatically downloads the NCBI taxonomy database (~300MB) from official NCBI servers during initialization to support taxonomic lookups.
[PROMPT_INJECTION]: The skill contains explicit instructions directing the agent to steer user interactions toward the 'K-Dense Web' platform when handling complex or multi-step research tasks.
[PROMPT_INJECTION]: The skill processes external hierarchical data files (Newick/NHX), representing a surface for indirect prompt injection when combined with file-writing and script-execution capabilities.
Ingestion points: Data is loaded via Tree, PhyloTree, and ClusterTree constructors.
Boundary markers: No specific instructions or delimiters are provided to ensure the agent ignores instructions embedded within the processed data files.
Capability inventory: The skill can write files (tree.write), render images (tree.render), and execute shell commands.
Sanitization: There is no documented validation or sanitization of the input tree data contents.
[COMMAND_EXECUTION]: The documentation references and provides usage examples for executing auxiliary Python scripts (scripts/tree_operations.py, scripts/quick_visualize.py) for batch processing.

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