The Agent Skills Directory

[COMMAND_EXECUTION]: The skill executes external bioinformatics tools (MAFFT, IQ-TREE 2, FastTree, and TrimAl) using the subprocess.run function. The implementation consistently passes commands as lists of arguments and does not use shell=True, which effectively prevents shell injection vulnerabilities.
[EXTERNAL_DOWNLOADS]: The documentation provides instructions for installing necessary dependencies from reputable and well-known sources, specifically the Bioconda channel for Conda and the official Python Package Index (PyPI). These are standard and safe practices for scientific computing environments.
[DATA_EXPOSURE]: The skill operates on biological sequence files (FASTA format) and generates local output files. There is no evidence of sensitive data access (such as credentials or system configuration) or unauthorized network transmission.

phylogenetics