What is bio-comparative-genomics-hgt-detection?

A bioinformatics workflow for detecting horizontal gene transfer, where a gene moves between unrelated organisms instead of being inherited from a parent. It combines sequence composition, similarity patterns, and evolutionary-tree evidence.

Use it to scan genomes for transferred genes, detect genomic islands, compare gene and species histories, and trace likely transfer sources.

It helps identify genes that may have been acquired from another organism and investigate their possible donors.

bio-comparative-genomics-hgt-detection — Skill for Claude Code and Cod

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add GPTomics/bioSkills --skill hgt-detection

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/hgt-detection/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/hgt-detection)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/hgt-detection"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/hgt-detection/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/hgt-detection"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/hgt-detection.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 189 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 8,870 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00189	$0.08870
Opus 5	$0.00095	$0.04435
Sonnet 5	$0.00038	$0.01774
Haiku 4.5	$0.00019	$0.00887

Measured 7d ago against content hash 2c77bf10df04, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

bio-comparative-genomics-hgt-detection scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/hgt_detection.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Runs shell commandslowCapability

Expected in a hook, worth knowing in a rule or an instructions file.

subprocess.run([

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-comparative-genomics-hgt-detection — 95% identical, 12 lines differ

comparative-genomics/hgt-detection/SKILL.md · 411 lines

How it starts

The opening of the file, as written. The whole thing — 411 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: HGTector 2.0b3+, AvP 1.0.4+, HGTphyloDetect 1.0+, ALE 1.0+ (ssolo/ALE github), GeneRax 2.1.3+, AleRax 1.2.0+ (Morel 2024), RANGER-DTL 2.0+, IslandViewer 4 (web), mobileOG-db 1.0+, MetaCHIP 1.10+, IQ-TREE 2.3.6+, BioPython 1.84+, DIAMOND 2.1.10+. Open Tree of Life and NCBI Taxonomy reference databases updated 2024-Q3 minimum for HGTector/AvP.

Before using code patterns, verify installed versions match. If versions differ:

Python: pip show hgtector then hgtector search --help
CLI: ALEml_undated --help, generax --help, alerax --help
DB: hgtector database --check for taxonomy version

If code throws Taxonomy ID not found, database version mismatch, or KeyError on NCBI taxids, refresh the local taxonomy dump (NCBI updates monthly). ALE/GeneRax expect newick gene trees with bootstraps; AleRax expects gene-tree distributions (uniform bootstrap samples or UFBoot trees).

Horizontal Gene Transfer Detection

"Are these genes horizontally acquired, and from where?" -> HGT signal lives in three orthogonal signal classes: composition (recent transfers carry donor codon usage; erodes by Lawrence-Ochman 1998 amelioration in ~50-200 Myr), phylogeny (gene tree nests within distant clade), and phyletic distribution (patchy taxonomic presence). No single class proves HGT; claims require concordance across at least two classes plus mandatory exclusion of contamination and differential gene loss (DGL). The most consequential failure mode in eukaryotic HGT detection is contamination passing all three classes silently (Boothby 2015 tardigrade "17% HGT" refuted by Koutsovoulos 2016; Crisp 2015 human "145 HGTs" refuted by Salzberg 2017 GB 18:85).

Python: hgtector search -> hgtector analyze for BLAST-distribution screen
Python: AvP (Koutsovoulos 2022 PLoS Comp Biol 18:e1010686) for eukaryotic phylogenetic HGT with automated tree workflow
CLI: ALEml_undated (Szöllősi 2013 Syst Biol 62:901), generax (Morel 2020 MBE 37:2763), alerax (Morel 2024 Bioinformatics 40:btae162) for prokaryote DTL reconciliation
Web: IslandViewer 4 (Bertelli 2017 NAR 45:W30) for bacterial genomic islands
CLI: metachip (Song 2019 Microbiome 7:36) for metagenomic HGT inference

Read the full file on GitHub · 411 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

7d ago First seen · 411 lines · 189 tokens per session scan A 2c77bf10df04

Subscribe to this mod's changes

bio-comparative-genomics-hgt-detection is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 189 tokens to every session and 8,870 once invoked, about $0.0009 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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bio-comparative-genomics-hgt-detection