The Agent Skills Directory

[COMMAND_EXECUTION]: The skill uses the subprocess module to run local bioinformatics binaries like MAFFT, IQ-TREE 2, and FastTree.
All command execution calls use list-based arguments rather than string interpolation, which effectively prevents shell injection vulnerabilities.
Parameters and file paths are handled as discrete arguments in the subprocess list.
[EXTERNAL_DOWNLOADS]: The documentation provides installation instructions for necessary dependencies via standard package managers.
Dependencies such as mafft, iqtree, and fasttree are recommended from the bioconda channel.
The Python library ete3 is recommended via pip.
These are well-established tools in the genomics and evolutionary biology communities.
[INDIRECT_PROMPT_INJECTION]: The skill processes external sequence data in FASTA format.
Analysis confirms that this data is passed directly to specialized binaries (MAFFT, etc.) which treat the sequences as raw data.
The skill does not interpolate untrusted sequence content into prompts for the AI agent, mitigating injection risks.

phylogenetics