The Agent Skills Directory

[SAFE]: The skill implements standard bioinformatics workflows for managing phylogenetic data. The instructions and scripts focus on reconciling species name mismatches and maintaining synchronization between tree files and annotation datasets.
[SAFE]: The provided Bash commands utilize common utilities like grep, sort, and comm for basic text comparison. These operations are limited to the local file system and do not involve network activity or elevated privileges.
[SAFE]: Python snippets for bulk editing iTOL files use standard file I/O operations and tab-delimited parsing. The logic is restricted to biological data manipulation and does not exhibit dynamic code execution or obfuscation.
[INDIRECT_PROMPT_INJECTION]: The skill is designed to ingest and process external data sources including Newick tree files (.nwk), CSV data, and iTOL text annotations.
Ingestion points: Reads content from Tree.nwk, Tree_final.nwk, and various ITOL annotation files in SKILL.md.
Boundary markers: None identified.
Capability inventory: Uses Bash, Grep, Glob, and Read tools; performs local file writes.
Sanitization: Uses regex and string splitting to parse biological names, providing inherent structural validation against non-conforming injection attempts. The risk is assessed as safe as this ingestion is essential to the skill's primary function and the processing logic is not susceptible to command interpretation.

phylogenetics