comparative-genomics-hgt-detection
comparative-genomics-hgt-detection is a Bioinformatics & life sciences skill for AI agents, published by swaruplab in the operon repository on GitHub. Skillspace rates comparative-genomics-hgt-detection F (45/100) and the safety scan rated it risky; the rating is based on static analysis only.
Risky. This skill has patterns associated with unsafe behaviour. Read the source carefully before running it.
Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.
- Grade
- F
- Quality
- 45 / 100
- Safety
- Risky
- GitHub stars
- 90
Unproven: rated by static analysis only, not yet compared head-to-head.
This rating describes the version of the repository we crawled; it may have changed since.
Our review
- Architecture
- 97 / 100
- Maturity
- Structured: ships references or scripts
- Security scan
- High-risk patterns
- License
- MIT
- Adoption
- Adopted by 0 other repositories, in 1 collections
What the scanner flagged
- executes shell/subprocess
Not checked yet
- Category is a classifier prediction; no model has read this skill yet
- Not judged on the rubric yet (not a contender in its category)
- No blind task eval yet
- Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
- Sibling files (scripts, references) not fetched; security scan covers SKILL.md only
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