Category:Science & Research · Sub-category: biology-medicine · Last updated:
Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata.
About this skill (catalog notes)
bio-epidemiological-genomics-transmission-inference includes at least one code block. At roughly 4,333 words the SKILL.md is on the longer end of the catalog distribution.
How bio-epidemiological-genomics-transmission-inference fits the catalog
bio-epidemiological-genomics-transmission-inference sits in the Science & Research category under the biology-medicine sub-topic in the ClaudSkills catalog. There are 10 related skills indexed alongside it; comparing a few before installing usually reveals which fits your workflow best.
These notes are auto-generated from features detected in the SKILL.md file and from this catalog's structure — they aren't part of the source repository.
What this skill does
bio-epidemiological-genomics-transmission-inference is a community-contributed Claude Code skill in the biology-medicine sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/ and loads when your prompt matches the skill's trigger.
Who uses this skill
The bio-epidemiological-genomics-transmission-inference Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 93,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).
Or just download SKILL.md directly and drop it into ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/. Claude Code auto-discovers it on next session.
Skills live at ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\bio-epidemiological-genomics-transmission-inference--skills-tran\SKILL.md on Windows. See the full install guide for step-by-step instructions.
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One-click install via the desktop app
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How do I install the bio-epidemiological-genomics-transmission-inference Claude Code skill?
Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.
What does the bio-epidemiological-genomics-transmission-inference skill do?
Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata.
Is this skill free to install?
Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.
When should I use the bio-epidemiological-genomics-transmission-inference skill?
Use bio-epidemiological-genomics-transmission-inference when your Claude Code task falls under the Science & Research category — specifically in the biology medicine area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use bio-epidemiological-genomics-transmission-inference" or describe the task and let Claude pick). Browse related skills at /category/science/.
What is a Claude Code skill and how does the bio-epidemiological-genomics-transmission-inference skill fit in?
A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. bio-epidemiological-genomics-transmission-inference is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at /learn/what-is-a-claude-skill/.
@misc{bio-epidemiological-genomics-transmission-inference--skills-tran-2026,
author = {bg-szy},
title = {bio-epidemiological-genomics-transmission-inference [Claude Code skill]},
year = {2026},
publisher = {ClaudSkills},
url = {https://claudskills.com/skills/bio-epidemiological-genomics-transmission-inference--skills-tran/}
}
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