tooluniverse-phylogenetics
Phylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree building (EBI_build_phylogenetic_tree) from your own sequences, plus tree analysis, treeness, saturation (PhyKIT), parsimony-informative sites, alignment gap analysis, DVMC, long-branch detection, BUSCO orthologs. Uses PhyKIT, Biopython, DendroPy. Use to align a set of sequences, build a tree from sequences or an alignment, or for phylogenetic tree QC, multi-gene phylogenomics, evolutionary-rate analysis, and comparative-genomics studies.
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Low
Low-risk findings worth noting
Low
Low-risk findings.
1 low severity finding. Worth noting, but not necessarily harmful.
W011: Third-party content exposure detected (indirect prompt injection risk).
What this means
The skill exposes the agent to untrusted, user-generated content from public third-party sources, creating a risk of indirect prompt injection. This includes browsing arbitrary URLs, reading social media posts or forum comments, and analyzing content from unknown websites.
Why it was flagged
Required runtime workflow reads outsider-authored free text from the user-provided `target_orthologs.txt` (and `scogs_*.zip`-extracted FASTA/Newick content that is treated as data), via `busco_target_orthologs.py` loading `targets_file` lines and parsing/extracting FASTA lengths.
- Repository
- mims-harvard/ToolUniverse
- Commit
089eb8e
- Audited
- Security analysis
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