The Agent Skills Directory

[SAFE]: The skill uses well-known bioinformatics libraries (Biopython, PhyKIT, DendroPy, scipy) for its core logic. These dependencies are standard in the field and used for their intended analytical purposes.
[EXTERNAL_DOWNLOADS]: The skill documentation lists standard Python packages (numpy, pandas, scipy, biopython, phykit, dendropy, ete3) as requirements. These are official packages hosted on well-known registries like PyPI.
[SAFE]: The Python scripts (format_alignment.py and tree_statistics.py) implement data processing logic using structural parsers and mathematical libraries. They do not utilize high-risk functions such as eval(), exec(), or subprocess calls for arbitrary command execution.
[SAFE]: The skill defines an ingestion surface for indirect prompt injection by processing external FASTA and Newick files. However, the risk is negligible as the skill lacks high-privilege capabilities such as networking or system-level command execution, and the data is processed by specialized bioinformatics parsers.
Ingestion points: load_alignment and load_tree functions in scripts/tree_statistics.py and scripts/format_alignment.py.
Boundary markers: Absent.
Capability inventory: Local file system read/write (via Biopython's AlignIO/Phylo) and statistical processing.
Sanitization: Relies on structural parsing logic within the Biopython and DendroPy libraries.

tooluniverse-phylogenetics